151
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Read DS, Gweon HS, Bowes MJ, Anjum MF, Crook DW, Chau KK, Shaw LP, Hubbard A, AbuOun M, Tipper HJ, Hoosdally SJ, Bailey MJ, Walker AS, Stoesser N. Dissemination and persistence of antimicrobial resistance (AMR) along the wastewater-river continuum. WATER RESEARCH 2024; 264:122204. [PMID: 39116608 DOI: 10.1016/j.watres.2024.122204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 07/15/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024]
Abstract
Antimicrobial resistance (AMR) is a global health hazard. Although clinical and agricultural environments are well-established contributors to the evolution and dissemination of AMR, research on wastewater treatment works (WwTWs) has highlighted their potential role as disseminators of AMR in freshwater environments. Using metagenomic sequencing and analysis, we investigated the changes in resistomes and associated mobile genetic elements within untreated wastewater influents and treated effluents of five WwTWs, and sediments collected from corresponding river environments in Oxfordshire, UK, across three seasonal periods within a year. Our analysis demonstrated a high diversity and abundance of antimicrobial resistance genes (ARGs) in untreated wastewater influents, reflecting the varied anthropogenic and environmental origins of wastewater. WwTWs effectively reduced AMR in the final effluent, with an average 87 % reduction in normalised ARG abundance and an average 63 % reduction in richness. However, wastewater effluents significantly impacted the antimicrobial resistome of the receiving rivers, with an average 543 % increase in ARG abundance and a 164 % increase in richness from upstream sediments to downstream sediments. The normalised abundance of the human gut-associated bacteriophage crAssphage was highly associated with both ARG abundance and richness. We observed seasonal variation in the resistome of raw influent which was not found in the effluent-receiving sediments. We illustrate the potential of WwTWs as focal points for disseminating ARGs and resistance-selecting chemicals, contributing to the elevation of environmental AMR. Our study emphasises the need for a comprehensive understanding of the anthropogenic impacts on AMR evolution and dissemination in wastewater and river environments, informing efforts to mitigate this growing public health crisis.
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Affiliation(s)
- Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK.
| | - H Soon Gweon
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK; School of Biological Sciences, University of Reading, Reading, UK
| | - Michael J Bowes
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey KT15 3NB, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Liam P Shaw
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Alasdair Hubbard
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Biosciences, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey KT15 3NB, UK
| | - Holly J Tipper
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | | | - Mark J Bailey
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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152
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Du P, Li J, Hua M, Zhu L, Chen C, Zeng H. Potential Contributions of Human Endogenous Retroviruses in Innate Immune Memory. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:1225-1233. [PMID: 39230265 DOI: 10.4049/jimmunol.2300411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/08/2024] [Indexed: 09/05/2024]
Abstract
The phenomenon wherein innate immune cells adopt long-term inflammatory phenotypes following the first stimuli is named trained immunity and can improve host defense against infections. Transcriptional and epigenetic reprogramming are critical mechanisms of trained immunity; however, the regulatory networks are not entirely clear at present. The human endogenous retroviruses (HERVs) provide large amounts of transcriptional regulators in the regulatory pathways. In this study, we analyzed published large omics data to explore the roles of such "dark matter" of the human genome in trained and tolerant macrophages. We collected 80 RNA sequencing data and 62 sequencing data to detect histone modifications and active regulatory regions from nine published studies on trained and tolerant macrophages. By analyzing the characteristics of transcription and epigenetic modification of HERVs, as well as their association with gene expression, we found that 15.3% of HERVs were transcribed nonrandomly from noncoding regions and enriched in specific HERV families and specific chromosomes, such as chromosomes 11, 15, 17, and 19, and they were highly related with the expression of adjacent genes. We found that 295 differentially expressed HERVs are located in 50-kbp flanking regions of 142 differentially expressed genes. We found epigenetic changes of these HERVs and that overlap with predicted enhancers and identified 35 enhancer-like HERVs. The related genes were highly involved in the activation and inflammatory responses, such as the TLR pathway. Other pathways including phosphoinositide signaling and transport of folate and K+ might be also related with trained immunity, which require further study. These results demonstrated that HERVs might play important roles in trained immunity.
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Affiliation(s)
- Pengcheng Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China; and
| | - Jiarui Li
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mingxi Hua
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Liuluan Zhu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China; and
| | - Chen Chen
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hui Zeng
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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153
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Bailey AS, Fuller MT. YTHDC2 serves a distinct late role in spermatocytes during germ cell differentiation. Proc Natl Acad Sci U S A 2024; 121:e2309548121. [PMID: 39378093 DOI: 10.1073/pnas.2309548121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/05/2024] [Indexed: 10/10/2024] Open
Abstract
Posttranscriptional regulation of gene expression by RNA-binding proteins can enhance the speed and robustness of cell state transitions by controlling RNA stability, localization, or if, when, or where mRNAs are translated. The RNA helicase YTHDC2 is required to shut down components of the mitotic program to facilitate a proper switch from mitosis to meiosis in mouse germ cells. Here, we show that YTHDC2 has a second essential role in promoting meiotic progression in late spermatocytes. Inducing conditional knockout of Ythdc2 during the first wave of spermatogenesis, after initiation of meiotic prophase, allowed YTHDC2-deficient germ cells to advance to the pachytene stage and properly express many meiotic markers. However, the YTHDC2-deficient spermatocytes mis-expressed a number of genes, some up-regulated and some down-regulated, failed to transition to the diplotene stage, and then quickly died. Coimmunoprecipitation experiments revealed that YTHDC2 interacts with several RNA-binding proteins in early or late spermatocytes, with many of the interacting proteins, including MEIOC, localizing to granules, similar to YTHDC2. Our findings suggest that YTHDC2 collaborates with other RNA granule components to facilitate proper progression of germ cells through multiple steps of meiosis via mechanisms influencing posttranscriptional regulation of RNAs.
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Affiliation(s)
- Alexis S Bailey
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Margaret T Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
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154
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Dudley JS, Renfree MB, Wagner GP, Griffith OW. The extension of mammalian pregnancy required taming inflammation: Independent evolution of extended placentation in the tammar wallaby. Proc Natl Acad Sci U S A 2024; 121:e2310047121. [PMID: 39378090 DOI: 10.1073/pnas.2310047121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/24/2024] [Indexed: 10/10/2024] Open
Abstract
In the first live-bearing mammals, pregnancy was likely short and ended with a brief period of inflammatory maternal-fetal interaction. This mode of reproduction has been retained in many marsupials. While inflammation is key to successful implantation in eutherians, a key innovation in eutherians is the ability to switch off this inflammation after it has been initiated. This extended period, in which inflammation is suppressed, likely allowed for an extended period of placentation. Extended placentation has evolved independently in one lineage of marsupials, the macropodids (wallabies and kangaroos), with placentation lasting beyond the 2 to 4 d seen in other marsupial taxa, which allows us to investigate the role of inflammation response after attachment in the extension of placentation in mammals. By comparing gene expression changes at attachment in three marsupial species, the tammar wallaby, opossum, and fat-tailed dunnart, we show that inflammatory attachment is an ancestral feature of marsupial implantation. In contrast to eutherians, where attachment-related (quasi-) inflammatory reaction is even involved in epitheliochorial placentation (e.g., pig), this study found no evidence of a distinct attachment-related reaction in wallabies. Instead, only a small number of inflammatory genes are expressed at distinct points of gestation, including IL6 before attachment, LIF throughout placentation, and prostaglandins before birth. During parturition, a more distinct inflammatory reaction is detectable, likely involved in precipitating the parturition cascade similar to eutherians. We suggest that in wallaby, extended gestation became possible by avoiding an inflammatory attachment reaction, which is a different strategy than seen in eutherians.
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Affiliation(s)
- Jessica S Dudley
- Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
| | - Marilyn B Renfree
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520
- Yale Systems Biology Institute, Yale University, West Haven, CT 06520
- Department of Evolutionary Biology, University of Vienna, Vienna A-1030, Austria
| | - Oliver W Griffith
- Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
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155
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Xu H, Leng J, Liu F, Chen T, Qu J, Yang Y, Ning C, Ke X, Xiao B, Zhang Y, Sun L. Tumor microbiota of renal cell carcinoma affects clinical prognosis by influencing the tumor immune microenvironment. Heliyon 2024; 10:e38310. [PMID: 39397906 PMCID: PMC11470785 DOI: 10.1016/j.heliyon.2024.e38310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 09/05/2024] [Accepted: 09/22/2024] [Indexed: 10/15/2024] Open
Abstract
Despite reported influences of the intratumoral microbiome on cancer progression, its role in this subtype remains unclear. This study aimed to characterize the microbial landscape and signatures of kidney renal clear cell carcinoma using RNA-Seq data from The Cancer Genome Atlas. Following microbial decontamination, differential microbial analysis was conducted between tumorous and adjacent non-tumorous samples. Compared to non-tumorous samples, tumorous microbiota exhibited reduced α and β diversity and distinct phylum-level communities. Differential microbial analysis between patients exhibiting long and short overall survival revealed ten significant differential microbial genera, with six genera correlating with a positive prognosis (Plasmodium, Babesia, Toxoplasma, Cytobacillus, Alicyclobacillus, Verrucomicrobium) and four with a negative prognosis (Colletotrichum, Leuconostoc, Gluconobacter, and Parabacteroides). Employing Cox regression analysis and support vector machines, a prognosis-related microbiome risk signature was developed, achieving an AUC of 0.809. Based on this risk signature, two microbiome-based subtypes were found to be significantly associated with distinct clinical prognoses and immune microenvironments. These findings were corroborated by significant correlations between prognostic-relevant microorganisms and 30 immune-related differentially expressed genes. Specifically, microbial genera associated with a negative prognosis were linked to a pro-tumor acute inflammatory immune response, whereas genera related to a positive prognosis were associated with an anti-tumor adaptive immune response. In conclusion, microbiome-based subtyping revealed correlations between tumor microbiome, clinical prognosis, and tumor microenvironment, indicating intratumoral microbiota as a promising prognostic biomarker for kidney renal clear cell carcinoma.
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Affiliation(s)
- Hengyi Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, China
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Jingze Leng
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Fengshuo Liu
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Tianxiang Chen
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Jiangming Qu
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Yufan Yang
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Chun Ning
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Xindi Ke
- Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Bin Xiao
- Department of Spine Surgery, Beijing Jishuitan Hospital, Affiliated Hospital of Capital Medicine University, 100035, Beijing, China
| | - Yanbin Zhang
- Department of Spine Surgery, Beijing Jishuitan Hospital, Affiliated Hospital of Capital Medicine University, 100035, Beijing, China
| | - Lejia Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 210029, Nanjing, China
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156
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Li R, Qu J, Yan K, Chen Y, Zhao X, Liu Z, Xie M, Zhang Q, He Y, Niu J, Qi J. Deciphering dynamic interactions between spermatozoa and the ovarian microenvironment through integrated multi-omics approaches in viviparous Sebastes schlegelii. Development 2024; 151:dev202224. [PMID: 38572957 DOI: 10.1242/dev.202224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
The ovarian microenvironment plays a crucial role in ensuring the reproductive success of viviparous teleosts. However, the molecular mechanism underlying the interaction between spermatozoa and the ovarian microenvironment has remained elusive. This study aimed to contribute to a better understanding of this process in black rockfish (Sebastes schlegelii) using integrated multi-omics approaches. The results demonstrated significant upregulation of ovarian complement-related proteins and pattern recognition receptors, along with remodeling of glycans on the surface of spermatozoa at the early spermatozoa-storage stage (1 month after mating). As spermatozoa were stored over time, ovarian complement proteins were progressively repressed by tryptophan and hippurate, indicating a remarkable adaptation of spermatozoa to the ovarian microenvironment. Before fertilization, a notable upregulation of cellular junction proteins was observed. The study revealed that spermatozoa bind to ZPB2a protein through GSTM3 and that ZPB2a promotes spermatozoa survival and movement in a GSTM3-dependent manner. These findings shed light on a key mechanism that influences the dynamics of spermatozoa in the female reproductive tract, providing valuable insights into the molecular networks regulating spermatozoa adaptation and survival in species with internal fertilization.
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Affiliation(s)
- Rui Li
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jiangbo Qu
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Kai Yan
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Ying Chen
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xi Zhao
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Zhiying Liu
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Mengxi Xie
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Quanqi Zhang
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yan He
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jingjing Niu
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jie Qi
- MOE Key Laboratory of Marine Genetics and Breeding/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
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157
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Li J, Yang P, Fu H, Li J, Wang Y, Zhu K, Yu J, Li J. Transcriptome analysis reveals key regulatory networks and genes involved in the acquisition of cold stress memory in pepper seedlings. BMC PLANT BIOLOGY 2024; 24:959. [PMID: 39396950 DOI: 10.1186/s12870-024-05660-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 10/01/2024] [Indexed: 10/15/2024]
Abstract
Temperature is an important limiting factor in the counter-seasonal cultivation of pepper. Currently, there are no studies on transcriptomic analysis of 'cold stress memory' in pepper. In this study, in order to understand the mechanism of 'cold stress memory' in pepper (Capsicum annuum L.), seedlings were subjected to the following treatments: normal temperature treatment (P0), the first cold treatment for 3 days (P3), the recovery temperature treatment for 3 days (R3), and another cold treatment for 3 days (RP3). The results showed that P3 plants wilted the most, RP3 the second and R3 the least. Leaf reactive oxygen species (ROS) and electrolyte leakage were the most in P3, the second in RP3 and the least in R3. In addition, RP3 had the highest accumulation of zeaxanthin, violaxanthin and β-cryptoxanthin, followed by P3, and R3 had the least. These results suggest that pepper seedlings are characterized by 'cold stress memory'. Transcriptomics was used to analyze the key genes and transcription factors involved in the biosynthesis of zeaxanthin, violaxanthin and β-cryptoxanthin during the formation of 'cold stress memory'. This study provides candidate genes and transcription factors for an in-depth study of the cold tolerance mechanism in pepper.
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Affiliation(s)
- Jian Li
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, China
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661100, China
| | - Ping Yang
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661100, China
| | - Hongbo Fu
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661100, China
| | - Juan Li
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661100, China
- College of Horticulture and Forestry, Tarim University, Alar, 843300, China
| | - Yanzhuang Wang
- College of Horticulture and Forestry, Tarim University, Alar, 843300, China
| | - Keyan Zhu
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, China
| | - Jihua Yu
- College of Horticulture, Gansu Agriculture University, Lanzhou, 730070, China.
| | - Jie Li
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, 661100, China.
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158
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Kamalakar A, Tobin B, Kaimari S, Robinson MH, Toma AI, Cha T, Chihab S, Moriarity I, Gautam S, Bhattaram P, Abramowicz S, Drissi H, Garcia A, Wood L, Goudy SL. Delivery of a Jagged1-PEG-MAL hydrogel with pediatric human bone cells regenerates critically sized craniofacial bone defects. eLife 2024; 13:RP92925. [PMID: 39401071 DOI: 10.7554/elife.92925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2024] Open
Abstract
Current treatments for congenital and acquired craniofacial (CF) bone abnormalities are limited and costly. Conventional methods involve surgical correction, short-term stabilization, and long-term bone grafting, which may include problematic allografts and limited autografts. While bone morphogenetic protein 2 (BMP2) has been used for bone regeneration, it can cause bone overgrowth and life-threatening inflammation. Bone marrow-derived mesenchymal stem cell therapies, though promising, are not Food and Drug Administration approved and are resource intensive. Thus, there is a need for effective, affordable, and less side-effect-prone bone regenerative therapies. Previous research demonstrated that JAGGED1 induces osteoblast commitment in murine cranial neural crest cells through a NOTCH-dependent non-canonical pathway involving JAK2-STAT5. We hypothesize that delivery of JAGGED1 and induction of its downstream NOTCH non-canonical signaling in pediatric human osteoblasts constitutes an effective bone regenerative treatment. Delivering pediatric human bone-derived osteoblast-like cells to an in vivo murine bone loss model of a critically sized cranial defect, we identified that JAGGED1 promotes human pediatric osteoblast commitment and bone formation through p70 S6K phosphorylation. This approach highlights the potential of JAGGED1 and its downstream activators as innovative treatments for pediatric CF bone loss.
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Affiliation(s)
- Archana Kamalakar
- Department of Pediatric Otolaryngology, Emory University, Atlanta, United States
| | - Brendan Tobin
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, United States
- School of Chemistry and Biomolecular Engineering, Georgia Tech College of Engineering, Atlanta, United States
| | - Sundus Kaimari
- Department of Pediatric Otolaryngology, Emory University, Atlanta, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, United States
| | - M Hope Robinson
- Department of Pediatric Otolaryngology, Emory University, Atlanta, United States
| | - Afra I Toma
- Department of Pediatric Otolaryngology, Emory University, Atlanta, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, United States
| | - Timothy Cha
- Department of Pediatric Otolaryngology, Emory University, Atlanta, United States
| | - Samir Chihab
- Department of Orthopedics, Emory University, Atlanta, United States
| | - Irica Moriarity
- Neuroscience Program in College of Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Surabhi Gautam
- Department of Orthopedics, Emory University, Atlanta, United States
| | - Pallavi Bhattaram
- Department of Orthopedics, Emory University, Atlanta, United States
- The Atlanta Veterans Affairs Medical Center Atlanta, Atlanta, United States
| | - Shelly Abramowicz
- Department of Pediatric Otolaryngology, Emory University, Atlanta, United States
- Department of Surgery, Division of Oral and Maxillofacial Surgery, Emory University, Atlanta, United States
| | - Hicham Drissi
- Department of Orthopedics, Emory University, Atlanta, United States
- The Atlanta Veterans Affairs Medical Center Atlanta, Atlanta, United States
- Department of Cell Biology, Emory University, Atlanta, United States
| | - Andres Garcia
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, United States
- George W. Woodruff School of Mechanical Engineering, Georgia Tech College of Engineering, Atlanta, United States
| | - Levi Wood
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, United States
- George W. Woodruff School of Mechanical Engineering, Georgia Tech College of Engineering, Atlanta, United States
| | - Steven L Goudy
- Department of Pediatric Otolaryngology, Children's Healthcare of Atlanta, Atlanta, United States
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159
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Villiers F, Suhail Y, Lee J, Hauser F, Hwang J, Bader JS, McKay JK, Peck SC, Schroeder JI, Kwak JM. Transcriptomic dynamics of ABA response in Brassica napus guard cells. STRESS BIOLOGY 2024; 4:43. [PMID: 39400760 DOI: 10.1007/s44154-024-00169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 04/22/2024] [Indexed: 10/15/2024]
Abstract
Drought has a significant, negative impact on crop production; and these effects are poised to increase with climate change. Plants acclimate to drought and water stress through diverse physiological responses, primarily mediated by the hormone abscisic acid (ABA). Because plants lose the majority of their water through stomatal pores on aerial surfaces of plants, stomatal closure is one of the rapid responses mediated by ABA to reduce transpirational water loss. The dynamic changes in the transcriptome of stomatal guard cells in response to ABA have been investigated in the model plant Arabidopsis thaliana. However, guard cell transcriptomes have not been analyzed in agronomically valuable crops such as a major oilseed crop, rapeseed. In this study, we investigated the dynamics of ABA-regulated transcriptomes in stomatal guard cells of Brassica napus and conducted comparison analysis with the transcriptomes of A. thaliana. We discovered changes in gene expression indicating alterations in a host of physiological processes, including stomatal movement, metabolic reprogramming, and light responses. Our results suggest the existence of both immediate and delayed responses to ABA in Brassica guard cells. Furthermore, the transcription factors and regulatory networks mediating these responses are compared to those identified in Arabidopsis. Our results imply the continuing evolution of ABA responses in Brassica since its divergence from a common ancestor, involving both protein-coding and non-coding nucleotide sequences. Together, our results will provide a basis for developing strategies for molecular manipulation of drought tolerance in crop plants.
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Affiliation(s)
- Florent Villiers
- Centre de Recherche de La Dargoire, Bayer CropScience, 69009, Lyon, France.
| | - Yasir Suhail
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Jade Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Felix Hauser
- Division of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jaeung Hwang
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - John K McKay
- Department of Bioagricultural Sciences, Colorado State University, Fort Collins, CO, 80523-1177, USA
| | - Scott C Peck
- Department of Biochemistry and Christopher S. Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA, 92093, USA
| | - June M Kwak
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
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160
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Shin J, Zielinski DC, Palsson BO. Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules. Nucleic Acids Res 2024; 52:11362-11377. [PMID: 39193902 DOI: 10.1093/nar/gkae742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024] Open
Abstract
Synthetic biology enables the reprogramming of cellular functions for various applications. However, challenges in scalability and predictability persist due to context-dependent performance and complex circuit-host interactions. This study introduces an iModulon-based engineering approach, utilizing machine learning-defined co-regulated gene groups (iModulons) as design parts containing essential genes for specific functions. This approach identifies the necessary components for genetic circuits across different contexts, enhancing genome engineering by improving target selection and predicting module behavior. We demonstrate several distinct uses of iModulons: (i) discovery of unknown iModulons to increase protein productivity, heat tolerance and fructose utilization; (ii) an iModulon boosting approach, which amplifies the activity of specific iModulons, improved cell growth under osmotic stress with minimal host regulation disruption; (iii) an iModulon rebalancing strategy, which adjusts the activity levels of iModulons to balance cellular functions, significantly increased oxidative stress tolerance while minimizing trade-offs and (iv) iModulon-based gene annotation enabled natural competence activation by predictably rewiring iModulons. Comparative experiments with traditional methods showed our approach offers advantages in efficiency and predictability of strain engineering. This study demonstrates the potential of iModulon-based strategies to systematically and predictably reprogram cellular functions, offering refined and adaptable control over complex regulatory networks.
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Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
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161
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Li Z, Li Q, Peng Q, Smagghe G, Li G. RNAi of nuclear receptor E78 inhibits the cuticle formation in the molting process of spider mite, Tetranychus urticae. PEST MANAGEMENT SCIENCE 2024. [PMID: 39400455 DOI: 10.1002/ps.8484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 09/29/2024] [Accepted: 10/01/2024] [Indexed: 10/15/2024]
Abstract
BACKGROUND The two-spotted spider mite, Tetranychus urticae, is an important pest mite in agriculture worldwide. E78, as a member of the nuclear receptor superfamily and a downstream responsive gene of ecdysteroids, plays a crucial role in regulating physiological behaviors such as development and reproduction in insects. However, its function in mites remains unclear. The aim of this study was to explore how E78 functions in the molting process of spider mites. RESULTS In this study, reverse transcription quantitative polymerase chain reaction (RT-qPCR) experiments to analyze the expression pattern of TuE78 during the development of Tetranychus urticae, demonstrated that the expression level of TuE78 was higher during the molting state than that after the completion of molting, and it reached a peak expression level when the deutonymph mites entered the molting stage. RNA interference (RNAi)-mediated gene-silencing of TuE78 resulted in 95% deutonymph mite molt failure. A series of analysis under a light microscope, and scanning and transmission electron microscopy revealed that RNAi mites died within the exuvium without ecdysis, and that apolysis had started but the new cuticle was thin and the typical cuticular lamellae were absent, indicating blockage of the post-apolysial processes and explaining molt failure. Hence, transcriptome sequencing confirmed that the expression of cuticle protein and lipid metabolism-related genes was significantly affected after TuE78 silencing. CONCLUSION This study demonstrated that TuE78 participates in the molting process of Tetranychus urticae by regulating the post-apolysial processes with the formation of new cuticle and successful ecdysis. This in turn suggests the potential of TuE78 as a target for pest mite control and provides a theoretical basis for further exploration of the molecular regulatory mechanism of spider mite molting. © 2024 Society of Chemical Industry. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- Zhuo Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
- Institute of Plant Health and Medicine, Guizhou University, Guiyang, China
| | - Qingyan Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
- Institute of Plant Health and Medicine, Guizhou University, Guiyang, China
| | - Qixiang Peng
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
- Institute of Plant Health and Medicine, Guizhou University, Guiyang, China
| | - Guy Smagghe
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
| | - Gang Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China
- Institute of Plant Health and Medicine, Guizhou University, Guiyang, China
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162
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Patel K, Barter M, Soul J, Clark P, Proctor C, Clark I, Young D, Shanley DP. Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis. eLife 2024; 12:RP89701. [PMID: 39401064 DOI: 10.7554/elife.89701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2024] Open
Abstract
Changes in chondrocyte gene expression can contribute to the development of osteoarthritis (OA), and so recognition of the regulative processes during chondrogenesis can lead to a better understanding of OA. microRNAs (miRNAs) are key regulators of gene expression in chondrocytes/OA, and we have used a combined experimental, bioinformatic, and systems biology approach to explore the multiple miRNA-mRNA interactions that regulate chondrogenesis. A longitudinal chondrogenesis bioinformatic analysis identified paralogues miR-199a-5p and miR-199b-5p as pro-chondrogenic regulators. Experimental work in human cells demonstrated alteration of miR-199a-5p or miR-199b-5p expression led to significant inverse modulation of key chondrogenic genes and extracellular matrix production. miR-199a/b-5p targets FZD6, ITGA3 and CAV1 were identified by inhibition experiments and verified as direct targets by luciferase assay. The experimental work was used to generate and parameterise a multi-miRNA 14-day chondrogenesis kinetic model to be used as a repository for the experimental work and as a resource for further investigation of this system. This is the first multi-miRNA model of a chondrogenesis-based system, and highlights the complex relationships between regulatory miRNAs, and their target mRNAs.
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Affiliation(s)
- Krutik Patel
- Campus for Ageing and Vitality, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Matt Barter
- Regenerative Medicine, Stem Cells, Transplantation, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jamie Soul
- Regenerative Medicine, Stem Cells, Transplantation, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Computational Biology Facility, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Peter Clark
- Campus for Ageing and Vitality, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Carole Proctor
- Campus for Ageing and Vitality, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Ian Clark
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - David Young
- Regenerative Medicine, Stem Cells, Transplantation, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Daryl P Shanley
- Campus for Ageing and Vitality, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
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163
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Wulff TF, Hahnke K, Lécrivain AL, Schmidt K, Ahmed-Begrich R, Finstermeier K, Charpentier E. Dynamics of diversified A-to-I editing in Streptococcus pyogenes is governed by changes in mRNA stability. Nucleic Acids Res 2024; 52:11234-11253. [PMID: 39087550 DOI: 10.1093/nar/gkae629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 07/01/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing plays an important role in the post-transcriptional regulation of eukaryotic cell physiology. However, our understanding of the occurrence, function and regulation of A-to-I editing in bacteria remains limited. Bacterial mRNA editing is catalysed by the deaminase TadA, which was originally described to modify a single tRNA in Escherichia coli. Intriguingly, several bacterial species appear to perform A-to-I editing on more than one tRNA. Here, we provide evidence that in the human pathogen Streptococcus pyogenes, tRNA editing has expanded to an additional tRNA substrate. Using RNA sequencing, we identified more than 27 editing sites in the transcriptome of S. pyogenes SF370 and demonstrate that the adaptation of S. pyogenes TadA to a second tRNA substrate has also diversified the sequence context and recoding scope of mRNA editing. Based on the observation that editing is dynamically regulated in response to several infection-relevant stimuli, such as oxidative stress, we further investigated the underlying determinants of editing dynamics and identified mRNA stability as a key modulator of A-to-I editing. Overall, our findings reveal the presence and diversification of A-to-I editing in S. pyogenes and provide novel insights into the plasticity of the editome and its regulation in bacteria.
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Affiliation(s)
- Thomas F Wulff
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | - Karin Hahnke
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
| | | | | | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, 10117 Berlin, Germany
- Institute for Biology, Humboldt University Berlin, 10115 Berlin, Germany
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164
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Lee HS, Lee J, An HJ, Sung MJ, Heo JH, Lee SY, Song YS. Mitophagy Defects Exacerbate Inflammation and Aberrant Proliferation in Lymphocytic Thyroiditis. Thyroid 2024. [PMID: 39397581 DOI: 10.1089/thy.2024.0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Background: Mitochondrial dysfunction in the thyroid due to defective mitophagy has been observed in lymphocytic thyroiditis (LT). However, the effect of impaired mitophagy on the pathogenesis of LT is not well understood. The aim of this study is to investigate the role of mitophagy dysregulation in the thyroid gland. Methods: We analyzed RNA sequencing data of human thyroid glands with/without LT from Genotype-Tissue Expression (GTEx; n = 653) and performed RNA sequencing in thyroid glands of phosphatase and tensin homolog-induced putative protein kinase 1 (Pink1) knock-out and wild-type mice. We evaluated the phenotypic and histopathologic characteristics of the human (n = 16) and mouse thyroids. Additionally, we assessed cell proliferation, reactive oxygen species (ROS) production, and cytokine secretion of human thyroid epithelial cells (HTori-3) treated with PINK1 siRNA or a mitophagy inhibitor. Results: We found that expression of PINK1, a key regulator of mitophagy, was compromised in human thyroids with LT. Thyroid glands of Pink1-deficient mice exhibited increased inflammatory responses and nodular hyperplasia. Furthermore, mitophagy defects led to the production of pro-inflammatory cytokines and ROS in thyroid cells, resulting in immune cell recruitment. Notably, these mitophagy defects upregulated both the RNA expression and protein secretion of amphiregulin (AREG), an epidermal growth factor receptor (EGFR) ligand, in thyroid cells, while decreasing the protein expression of cAMP response element-binding protein (CREB), a transcription factor that suppresses AREG transcription. Finally, we demonstrated that aberrant cell proliferation in thyroid cells, driven by mitophagy defects, was mitigated after treatment with cetuximab, an EGFR inhibitor. Conclusions: In this study, we observed that mitophagy defects in the thyroid not only intensify inflammation through the accumulation of ROS, cytokine production, and immune cell recruitment but also contribute to hyperplasia via the EGFR pathway, facilitated by increased secretion of AREG from thyroid cells.
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Affiliation(s)
- Han Sai Lee
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Science, Graduate School, CHA University, Seongnam, South Korea
| | - Jinju Lee
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Science, Graduate School, CHA University, Seongnam, South Korea
| | - Hyun-Ju An
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Min-Ji Sung
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Jin-Hyung Heo
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - So-Young Lee
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Young Shin Song
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Science, Graduate School, CHA University, Seongnam, South Korea
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
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165
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Mohammadi F, Beauparlant CJ, Bianco S, Droit A, Bertrand N, Rudkowska I. Ruminant Trans Fatty Acid Intake Modulates Inflammation Pathways in the Adipose Tissue Transcriptome of C57BL/6 Mice. Mol Nutr Food Res 2024:e2400290. [PMID: 39396377 DOI: 10.1002/mnfr.202400290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 09/05/2024] [Indexed: 10/15/2024]
Abstract
SCOPE The study aims to analyze transcriptomic profiles in adipose tissues postconsumption of elaidic acid (EA; trans-18:1n-9) and trans-palmitoleic acid (TPA; trans-16:1n-7), elucidating their different effects on inflammation and glucose metabolism. METHODS AND RESULTS Twenty C57BL/6 mice are divided into four groups. Each group receives one of the following formulations in drinking water: lecithin nanovesicles, nanovesicles containing either lecithin with EA or TPA (86:14 w/w), or water (control) for 28 days with a regular fat diet (18% calories from fat). Total RNA is extracted, and paired-end sequencing is performed. TPA intake alters the expression of 351 genes compared to EA intake, including 11 downregulated and 340 upregulated genes (fold change [FC] >1.5, p < 0.05). TPA compares to EA upregulated: Slc5a8, Lcn2, Csf3, Scube1, Mapk13, Bdkrb2, Ctla2a, Slc2a1, Oas3, Cx3cl1, Oas2, Nlrp6, Pycard, Cyba, Ddr1, and Prkab1 and downregulated Fas gene. These genes are related to the NOD-like receptor, lipid and atherosclerosis, IL-17 signaling, TNF, nonalcoholic fatty liver disease, cytokine-cytokine receptor interaction, adipocytokine, glucagon, insulin resistance, and inflammatory mediator regulation of TRP channels signaling. CONCLUSION TPA intake has a distinct impact on the regulation of inflammation and diabetes-related pathways in adipose tissue compared to EA.
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Affiliation(s)
- Farzad Mohammadi
- Endocrinology and Nephrology Unit, CHU de Québec-Université Laval Research Center, Québec, Canada
- Département de Kinésiologie, Université Laval, Québec, Canada
| | - Charles Joly Beauparlant
- Endocrinology and Nephrology Unit, CHU de Québec-Université Laval Research Center, Québec, Canada
| | - Stéphanie Bianco
- Endocrinology and Nephrology Unit, CHU de Québec-Université Laval Research Center, Québec, Canada
| | - Arnaud Droit
- Endocrinology and Nephrology Unit, CHU de Québec-Université Laval Research Center, Québec, Canada
| | - Nicolas Bertrand
- Endocrinology and Nephrology Unit, CHU de Québec-Université Laval Research Center, Québec, Canada
- Faculté de Pharmacie, Université Laval, Québec, QC, G1V0A6, Canada
| | - Iwona Rudkowska
- Endocrinology and Nephrology Unit, CHU de Québec-Université Laval Research Center, Québec, Canada
- Département de Kinésiologie, Université Laval, Québec, Canada
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166
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Frohn S, Haas FB, Chavez BG, Dreyer BH, Reiss EV, Ziplys A, Weichert H, Hiltemann S, Ugalde JM, Meyer AJ, D'Auria JC, Rensing SA, Schippers JHM. Evolutionary Conserved and Divergent Responses to Copper Zinc Superoxide Dismutase Inhibition in Plants. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39400938 DOI: 10.1111/pce.15198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 09/24/2024] [Accepted: 09/25/2024] [Indexed: 10/15/2024]
Abstract
After an initial evolution in a reducing environment, life got successively challenged by reactive oxygen species (ROS), especially during the great oxidation event (GOE) that followed the development of photosynthesis. Therefore, ROS are deeply intertwined into the physiological, morphological and transcriptional responses of most present-day organisms. Copper-zinc superoxide dismutases (CuZnSODs) evolved during the GOE and are present in charophytes and extant land plants, but nearly absent from chlorophytes. The chemical inhibitor of CuZnSOD, lung cancer screen 1 (LCS-1), could greatly facilitate the study of SODs in diverse plants. Here, we determined the impact of chemical inhibition of plant CuZnSOD activity, on plant growth, transcription and metabolism. We followed a comparative approach by using different plant species, including Marchantia Polymorpha and Physcomitrium patens, representing bryophytes, the sister lineage to vascular plants, and Arabidopsis thaliana. We show that LCS-1 causes oxidative stress in plants and that the inhibition of CuZnSODs provoked a similar core response that mainly impacted glutathione homoeostasis in all plant species analysed. That said, Physcomitrium and Arabidopsis, which contain multiple CuZnSOD isoforms showed a more complex and exacerbated response. In addition, an untargeted metabolomics approach revealed a specific metabolic signature for each plant species. Our comparative analysis exposes a conserved core response at the physiological and transcriptional level towards LCS-1, while the metabolic response largely varies. These differences correlate with the number and localization of the CuZnSOD isoforms present in each species.
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Affiliation(s)
- Stephanie Frohn
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Benjamin G Chavez
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Bernd H Dreyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Erik V Reiss
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Anne Ziplys
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Heiko Weichert
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Saskia Hiltemann
- Center for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - José M Ugalde
- Institute of Crop Science and Resource Conservation (INRES) - Chemical Signalling, University of Bonn, Bonn, Germany
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES) - Chemical Signalling, University of Bonn, Bonn, Germany
| | - John C D'Auria
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Center for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Jos H M Schippers
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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167
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Nicoletto RE, Holdcraft CJ, Yin AC, Retzbach EP, Sheehan SA, Greenspan AA, Laugier CM, Trama J, Zhao C, Zheng H, Goldberg GS. Effects of cadherin mediated contact normalization on oncogenic Src kinase mediated gene expression and protein phosphorylation. Sci Rep 2024; 14:23942. [PMID: 39397108 DOI: 10.1038/s41598-024-75449-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 10/04/2024] [Indexed: 10/15/2024] Open
Abstract
Nontransformed cells form heterotypic cadherin junctions with adjacent transformed cells to inhibit tumor cell growth and motility. Transformed cells must override this form of growth control, called "contact normalization", to invade and metastasize during cancer progression. Heterocellular cadherin junctions between transformed and nontransformed cells are needed for this process. However, specific mechanisms downstream of cadherin signaling have not been clearly elucidated. Here, we utilized a β-catenin reporter construct to determine if contact normalization affects Wnt signaling in transformed cells. β-catenin driven GFP expression in Src transformed mouse embryonic cells was decreased when cultured with cadherin competent nontransformed cells compared to transformed cells cultured with themselves, but not when cultured with cadherin deficient nontransformed cells. We also utilized a layered culture system to investigate the effects of oncogenic transformation and contact normalization on gene expression and oncogenic Src kinase mediated phosphorylation events. RNA-Seq analysis found that cadherin dependent contact normalization inhibited the expression of 22 transcripts that were induced by Src transformation, and increased the expression of 78 transcripts that were suppressed by Src transformation. Phosphoproteomic analysis of cells expressing a temperature sensitive Src kinase construct found that contact normalization decreased phosphorylation of 10 proteins on tyrosine residues that were phosphorylated within 1 h of Src kinase activation in transformed cells. Taken together, these results indicate that cadherin dependent contact normalization inhibits Wnt signaling to regulate oncogenic kinase activity and gene expression, particularly PDPN expression, in transformed cells in order to control tumor progression.
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Affiliation(s)
- Rachel E Nicoletto
- Rowan-Virtua School of Osteopathic Medicine, Rowan University, B330 Science Center, 2 Medical Center Dr., Stratford, NJ, 08084, USA
| | - Cayla J Holdcraft
- Rowan-Virtua School of Osteopathic Medicine, Rowan University, B330 Science Center, 2 Medical Center Dr., Stratford, NJ, 08084, USA
| | - Ariel C Yin
- Rowan-Virtua School of Osteopathic Medicine, Rowan University, B330 Science Center, 2 Medical Center Dr., Stratford, NJ, 08084, USA
| | - Edward P Retzbach
- Rowan-Virtua School of Osteopathic Medicine, Rowan University, B330 Science Center, 2 Medical Center Dr., Stratford, NJ, 08084, USA
| | - Stephanie A Sheehan
- Rowan-Virtua School of Osteopathic Medicine, Rowan University, B330 Science Center, 2 Medical Center Dr., Stratford, NJ, 08084, USA
| | - Amanda A Greenspan
- Rowan-Virtua School of Osteopathic Medicine, Rowan University, B330 Science Center, 2 Medical Center Dr., Stratford, NJ, 08084, USA
| | - Christopher M Laugier
- Rowan-Virtua School of Osteopathic Medicine, Rowan University, B330 Science Center, 2 Medical Center Dr., Stratford, NJ, 08084, USA
| | - Jason Trama
- Medical Diagnostic Laboratories, 2439 Kuser Rd, Hamilton Township, NJ, 08690, USA
| | - Caifeng Zhao
- Biological Mass Spectrometry Resources, Robert Wood Johnson Medical School, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Resources, Robert Wood Johnson Medical School, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Gary S Goldberg
- Rowan-Virtua School of Osteopathic Medicine, Rowan University, B330 Science Center, 2 Medical Center Dr., Stratford, NJ, 08084, USA.
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168
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Hemara LM, Chatterjee A, Yeh SM, Chen RKY, Hilario E, Lievre LL, Crowhurst RN, Bohne D, Arshed S, Patterson HR, Barrett-Manako K, Thomson S, Allan AC, Brendolise C, Chagné D, Templeton MD, Tahir J, Jayaraman J. Identification and Characterization of Innate Immunity in Actinidia melanandra in Response to Pseudomonas syringae pv. actinidiae. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39400369 DOI: 10.1111/pce.15189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/12/2024] [Accepted: 09/19/2024] [Indexed: 10/15/2024]
Abstract
Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) has decimated kiwifruit orchards growing susceptible kiwifruit Actinidia chinensis varieties. Effector loss has occurred recently in Psa3 isolates from resistant kiwifruit germplasm, resulting in strains capable of partially overcoming resistance present in kiwiberry vines (Actinidia arguta, Actinidia polygama, and Actinidia melanandra). Diploid male A. melanandra recognises several effectors, sharing recognition of at least one avirulence effector (HopAW1a) with previously studied tetraploid kiwiberry vines. Sequencing and assembly of the A. melanandra genome enabled the characterisation of the transcriptomic response of this non-host to wild-type and genetic mutants of Psa3. A. melanandra appears to mount a classic effector-triggered immunity (ETI) response to wildtype Psa3 V-13, as expected. Surprisingly, the type III secretion (T3SS) system-lacking Psa3 V-13 ∆hrcC strain did not appear to trigger pattern-triggered immunity (PTI) despite lacking the ability to deliver immunity-suppressing effectors. Contrasting the A. melanandra responses to an effectorless Psa3 V-13 ∆33E strain and to Psa3 V-13 ∆hrcC suggested that PTI triggered by Psa3 V-13 was based on the recognition of the T3SS itself. The characterisation of both ETI and PTI branches of innate immunity responses within A. melanandra further enables breeding for durable resistance in future kiwifruit cultivars.
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Affiliation(s)
- Lauren M Hemara
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Abhishek Chatterjee
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Shin-Mei Yeh
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Ronan K Y Chen
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Liam Le Lievre
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ross N Crowhurst
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Deborah Bohne
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Saadiah Arshed
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Haileigh R Patterson
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Kelvina Barrett-Manako
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Lincoln Research Centre, New Zealand
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Cyril Brendolise
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Matthew D Templeton
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Jibran Tahir
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
| | - Jay Jayaraman
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, New Zealand
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169
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Liu JW, Zhang ZQ, Zhu ZC, Li K, Xu Q, Zhang J, Cheng XW, Li H, Sun Y, Wang JJ, Hu LL, Xiong ZQ, Zhu Y. Loss of TET Activity in the Postnatal Mouse Brain Perturbs Synaptic Gene Expression and Impairs Cognitive Function. Neurosci Bull 2024:10.1007/s12264-024-01302-2. [PMID: 39395911 DOI: 10.1007/s12264-024-01302-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 06/13/2024] [Indexed: 10/14/2024] Open
Abstract
Conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) family proteins leads to the accumulation of 5hmC in the central nervous system; however, the role of 5hmC in the postnatal brain and how its levels and target genes are regulated by TETs remain elusive. We have generated mice that lack all three Tet genes specifically in postnatal excitatory neurons. These mice exhibit significantly reduced 5hmC levels, altered dendritic spine morphology within brain regions crucial for cognition, and substantially impaired spatial and associative memories. Transcriptome profiling combined with epigenetic mapping reveals that a subset of genes, which display changes in both 5hmC/5mC levels and expression patterns, are involved in synapse-related functions. Our findings provide insight into the role of postnatally accumulated 5hmC in the mouse brain and underscore the impact of 5hmC modification on the expression of genes essential for synapse development and function.
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Affiliation(s)
- Ji-Wei Liu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Ze-Qiang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Chuan Zhu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Kui Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 20031, China
- Lingang Laboratory, Shanghai, 201602, China
| | - Qiwu Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 20031, China
- Lingang Laboratory, Shanghai, 201602, China
| | - Jing Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Xue-Wen Cheng
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Han Li
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Ying Sun
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Ji-Jun Wang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Lu-Lu Hu
- Fudan University Institutes of Biomedical Sciences, Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Zhi-Qi Xiong
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 20031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201602, China.
| | - Yongchuan Zhu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
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170
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Willis C, White JD, Minto MS, Quach BC, Han S, Tao R, Shin JH, Deep-Soboslay A, Hyde TM, Mayfield RD, Webb BT, Johnson EO, Kleinman JE, Bierut LJ, Hancock DB. Gene expression differences associated with alcohol use disorder in human brain. Mol Psychiatry 2024:10.1038/s41380-024-02777-1. [PMID: 39394458 DOI: 10.1038/s41380-024-02777-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 09/25/2024] [Accepted: 09/30/2024] [Indexed: 10/13/2024]
Abstract
Excessive alcohol consumption is a leading cause of preventable death worldwide. To improve understanding of neurobiological mechanisms associated with alcohol use disorder (AUD) in humans, we compared gene expression data from deceased individuals with and without AUD across two addiction-relevant brain regions: the nucleus accumbens (NAc) and dorsolateral prefrontal cortex (DLPFC). Bulk RNA-seq data from NAc and DLPFC (N ≥50 with AUD, ≥46 non-AUD) were analyzed for differential gene expression using modified negative binomial regression adjusting for technical and biological covariates. The region-level results were meta-analyzed with those from an independent dataset (NNAc = 28 AUD, 29 non-AUD; NPFC = 66 AUD, 77 non-AUD). We further tested for heritability enrichment of AUD-related phenotypes, gene co-expression networks, gene ontology enrichment, and drug repurposing. We identified 176 differentially expressed genes (DEGs; 12 in both regions, 78 in NAc only, 86 in DLPFC only) for AUD in our new dataset. After meta-analyzing with published data, we identified 476 AUD DEGs (25 in both regions, 29 in NAc only, 422 in PFC only). Of these DEGs, 17 were significant when looked up in GWAS of problematic alcohol use or drinks per week. Gene co-expression analysis showed both concordant and unique gene networks across brain regions. We also identified 29 and 436 drug compounds that target DEGs from our meta-analysis in NAc and PFC, respectively. This study identified robust AUD-associated DEGs, contributing novel neurobiological insights into AUD and highlighting genes targeted by known drug compounds, generating opportunity for drug repurposing to treat AUD.
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Affiliation(s)
- Caryn Willis
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA.
| | - Julie D White
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Melyssa S Minto
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Bryan C Quach
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Shizhong Han
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
| | - Ran Tao
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
| | | | - Thomas M Hyde
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - Bradley T Webb
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development (LIBD), Baltimore, MD, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Dana B Hancock
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
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171
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Paik H, Oh C, Hussain S, Seo S, Park SW, Ko TL, Lee A. ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect. Database (Oxford) 2024; 2024:baae111. [PMID: 39395186 PMCID: PMC11470751 DOI: 10.1093/database/baae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/23/2024] [Accepted: 09/25/2024] [Indexed: 10/14/2024]
Abstract
The development of therapeutic agents has mainly focused on designing small molecules to modulate target proteins or genes which are conventionally druggable. Therefore, targeted protein degradation (TPD) for undruggable cases has emerged as promising pharmaceutical approach. TPD, often referred PROTACs (PROteolysis TArgeting Chimeras), uses a linker to degrade target proteins by hijacking the ubiquitination system. Therefore, unravel the relationship including reversal and co-expression between E3 ligands and other possible target genes in various human tissues is essential to mitigate off-target effects of TPD. Here, we developed the atlas of E3 ligases in human tissues (ELiAH), to prioritize E3 ligase-target gene pairs for TPD. Leveraging over 2900 of RNA-seq profiles consisting of 11 human tissues from the GTEx (genotype-tissue expression) consortium, users of ELiAH can identify tissue-specific genes and E3 ligases (FDR P-value of Mann-Whitney test < .05). ELiAH unravels 933 830 relationships consisting of 614 E3 ligases and 20 924 of expressed genes considering degree of tissue specificity, which are indispensable for ubiquitination based TPD development. In addition, docking properties of those relationships are also modeled using RosettaDock. Therefore, ELiAH presents comprehensive repertoire of E3 ligases for ubiquitination-based TPD drug development avoiding off-target effects. Database URL: https://eliahdb.org.
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Affiliation(s)
- Hyojung Paik
- Center for Supercomputing Application, Korea Institute of Science and Technology Information (KISTI), 245 Daehak-ro, Daejeon 34141, South Korea
- Center for Biomedical Computing, Korea Institute of Science and Technology Information (KISTI), 245 Daehak-ro, Daejeon 34141, South Korea
- Department of Data and HPC Science, University of Science and Technology (UST), 245 Daehak-ro, Daejeon 34141, South Korea
| | - Chunryong Oh
- Center for Supercomputing Application, Korea Institute of Science and Technology Information (KISTI), 245 Daehak-ro, Daejeon 34141, South Korea
- Center for Biomedical Computing, Korea Institute of Science and Technology Information (KISTI), 245 Daehak-ro, Daejeon 34141, South Korea
- Department of Data and HPC Science, University of Science and Technology (UST), 245 Daehak-ro, Daejeon 34141, South Korea
| | - Sajid Hussain
- Department of Applied AI, University of Science and Technology (UST), 245 Daehak-ro, Daejeon 34141, South Korea
| | - Sangjae Seo
- Center for Supercomputing Application, Korea Institute of Science and Technology Information (KISTI), 245 Daehak-ro, Daejeon 34141, South Korea
| | - Soon Woo Park
- Center for Nanotubes and Nanostructured Composites, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, South Korea
| | - Tae Lyun Ko
- Center for Biomedical Computing, Korea Institute of Science and Technology Information (KISTI), 245 Daehak-ro, Daejeon 34141, South Korea
- Department of Data and HPC Science, University of Science and Technology (UST), 245 Daehak-ro, Daejeon 34141, South Korea
| | - Ari Lee
- Center for Supercomputing Application, Korea Institute of Science and Technology Information (KISTI), 245 Daehak-ro, Daejeon 34141, South Korea
- Center for Biomedical Computing, Korea Institute of Science and Technology Information (KISTI), 245 Daehak-ro, Daejeon 34141, South Korea
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172
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Romero R, Chu T, González Robles TJ, Smith P, Xie Y, Kaur H, Yoder S, Zhao H, Mao C, Kang W, Pulina MV, Lawrence KE, Gopalan A, Zaidi S, Yoo K, Choi J, Fan N, Gerstner O, Karthaus WR, DeStanchina E, Ruggles KV, Westcott PMK, Chaligné R, Pe'er D, Sawyers CL. The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1. NATURE CANCER 2024:10.1038/s43018-024-00838-6. [PMID: 39394434 DOI: 10.1038/s43018-024-00838-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 09/06/2024] [Indexed: 10/13/2024]
Abstract
Lineage plasticity is a hallmark of cancer progression that impacts therapy outcomes, yet the mechanisms mediating this process remain unclear. Here, we introduce a versatile in vivo platform to interrogate neuroendocrine lineage transformation throughout prostate cancer progression. Transplanted mouse prostate organoids with human-relevant driver mutations (Rb1-/-; Trp53-/-; cMyc+ or Pten-/-; Trp53-/-; cMyc+) develop adenocarcinomas, but only those with Rb1 deletion advance to aggressive, ASCL1+ neuroendocrine prostate cancer (NEPC) resistant to androgen receptor signaling inhibitors. Notably, this transition requires an in vivo microenvironment not replicated by conventional organoid culture. Using multiplexed immunofluorescence and spatial transcriptomics, we reveal that ASCL1+ cells arise from KRT8+ luminal cells, progressing into transcriptionally heterogeneous ASCL1+;KRT8- NEPC. Ascl1 loss in established NEPC causes transient regression followed by recurrence, but its deletion before transplantation abrogates lineage plasticity, resulting in castration-sensitive adenocarcinomas. This dynamic model highlights the importance of therapy timing and offers a platform to identify additional lineage plasticity drivers.
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Affiliation(s)
- Rodrigo Romero
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tinyi Chu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tania J González Robles
- Institute of Systems Genetics, Department of Precision Medicine, NYU Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Perianne Smith
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yubin Xie
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Harmanpreet Kaur
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sara Yoder
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Huiyong Zhao
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chenyi Mao
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenfei Kang
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria V Pulina
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kayla E Lawrence
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuradha Gopalan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Genitourinary Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kwangmin Yoo
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Ning Fan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olivia Gerstner
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wouter R Karthaus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa DeStanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelly V Ruggles
- Institute of Systems Genetics, Department of Precision Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Ronan Chaligné
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Dana Pe'er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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173
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Bullert AJ, Wang H, Valenzuela AE, Neier K, Wilson RJ, Badley JR, LaSalle JM, Hu X, Lein PJ, Lehmler HJ. Interactions of Polychlorinated Biphenyls and Their Metabolites with the Brain and Liver Transcriptome of Female Mice. ACS Chem Neurosci 2024. [PMID: 39392776 DOI: 10.1021/acschemneuro.4c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2024] Open
Abstract
Exposure to polychlorinated biphenyls (PCBs) is linked to neurotoxic effects. This study aims to close knowledge gaps regarding the specific modes of action of PCBs in female C57BL/6J mice (>6 weeks) orally exposed for 7 weeks to a human-relevant PCB mixture (MARBLES mix) at 0, 0.1, 1, and 6 mg/kg body weight/day. PCB and hydroxylated PCB (OH-PCBs) levels were quantified in the brain, liver, and serum; RNA sequencing was performed in the striatum, prefrontal cortex, and liver, and metabolomic analyses were performed in the striatum. Profiles of PCBs but not their hydroxylated metabolites were similar in all tissues. In the prefrontal cortex, PCB exposure activated the oxidative phosphorylation respiration pathways, while suppressing the axon guidance pathway. PCB exposure significantly changed the expression of genes associated with neurodevelopmental and neurodegenerative diseases in the striatum, impacting pathways like growth hormone synthesis and dendrite development. PCBs did not affect the striatal metabolome. In contrast to the liver, which showed activation of metabolic processes following PCB exposure and the induction of cytochrome P450 enzymes, the expression of xenobiotic processing genes was not altered by PCB exposure in either brain region. Network analysis revealed complex interactions between individual PCBs (e.g., PCB28 [2,4,4'-trichlorobiphenyl]) and their hydroxylated metabolites and specific differentially expressed genes (DEGs), underscoring the need to characterize the association between specific PCBs and DEGs. These findings enhance the understanding of PCB neurotoxic mechanisms and their potential implications for human health.
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Affiliation(s)
- Amanda J Bullert
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa 52242, United States
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, Iowa 52242, United States
| | - Hui Wang
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa 52242, United States
| | - Anthony E Valenzuela
- Department of Molecular Biosciences, University of California, Davis, California 95616, United States
| | - Kari Neier
- Department of Medical Microbiology and Immunology, University of California, Davis, California 95616, United States
| | - Rebecca J Wilson
- Department of Molecular Biosciences, University of California, Davis, California 95616, United States
| | - Jessie R Badley
- Department of Molecular Biosciences, University of California, Davis, California 95616, United States
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, University of California, Davis, California 95616, United States
| | - Xin Hu
- Gangarosa Department of Environmental Health, Emory University, Atlanta, Georgia 30329, United States
| | - Pamela J Lein
- Department of Molecular Biosciences, University of California, Davis, California 95616, United States
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa 52242, United States
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, Iowa 52242, United States
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174
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Panten J, Del Prete S, Cleland JP, Saunders LM, van Riet J, Schneider A, Ginno P, Schneider N, Koch ML, Chen X, Gerstung M, Stegle O, Arnold AP, Turner JMA, Heard E, Odom DT. Four Core Genotypes mice harbour a 3.2MB X-Y translocation that perturbs Tlr7 dosage. Nat Commun 2024; 15:8814. [PMID: 39394207 PMCID: PMC11470063 DOI: 10.1038/s41467-024-52640-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 09/13/2024] [Indexed: 10/13/2024] Open
Abstract
The Four Core Genotypes (FCG) is a mouse model system used to disentangle the function of sex chromosomes and hormones. We report that a copy of a 3.2 MB region of the X chromosome has translocated to the YSry- chromosome and thus increased the expression of X-linked genes including the single-stranded RNA sensor and autoimmune disease mediator Tlr7. This previously-unreported X-Y translocation complicates the interpretation of studies reliant on C57BL/6J FCG mice.
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Affiliation(s)
- Jasper Panten
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefania Del Prete
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - James P Cleland
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Lauren M Saunders
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Job van Riet
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Artificial Intelligence in Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Schneider
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Ginno
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina Schneider
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marie-Luise Koch
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xuqi Chen
- Department of Integrative Biology & Physiology, University of California, Los Angeles, USA
| | - Moritz Gerstung
- Division of Artificial Intelligence in Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Arthur P Arnold
- Department of Integrative Biology & Physiology, University of California, Los Angeles, USA
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Edith Heard
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Collège de France, Paris, France.
| | - Duncan T Odom
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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175
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Alexander SE, Gatto B, Knowles OE, Williams RM, Fiebig KN, Jansons P, Della Gatta PA, Garnham A, Eynon N, Wadley GD, Aisbett B, Hiam D, Lamon S. Bioavailable testosterone and androgen receptor activation, but not total testosterone, are associated with muscle mass and strength in females. J Physiol 2024. [PMID: 39393048 DOI: 10.1113/jp286803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 09/05/2024] [Indexed: 10/13/2024] Open
Abstract
Testosterone, the major androgen, influences the reproductive and non-reproductive systems in males and females via binding to the androgen receptor (AR). Both circulating endogenous testosterone and muscle AR protein content are positively associated with muscle mass and strength in males, but there is no such evidence in females. Here, we tested whether circulating testosterone levels were associated with muscle mass, function, or the muscle anabolic response to resistance training in pre-menopausal females. Twenty-seven pre-menopausal, untrained females (aged 23.5 ± 4.8 years) underwent a 12-week resistance training programme. Muscle strength, size, power, and plasma and urine androgen hormone levels were measured. Skeletal muscle biopsies were collected before and after the training programme to quantify the effect of resistance training on AR content and nuclear localisation. Primary muscle cell lines were cultured from a subset (n = 6) of the participants' biopsies and treated with testosterone to investigate its effect on myotube diameter, markers of muscle protein synthesis and AR cellular localisation. Physiological levels of total testosterone were not associated with muscle mass or strength at baseline or with the changes in muscle mass and strength that occurred in response to resistance training in our cohort of pre-menopausal females. In contrast, bioavailable testosterone and the proportion of nuclear-localised AR were positively associated with skeletal muscle mass and strength in pre-menopausal females. In vitro, supra-physiological doses of testosterone increased myocyte diameter, but this did not occur via the Akt/mTOR pathway as previously suggested. Instead, we show a marked increase in AR nuclear localisation with testosterone administration in vitro. KEY POINTS: Total circulating testosterone was not related to muscle mass or strength before or after resistance training in pre-menopausal females. Bioavailable testosterone was positively related to exercise-induced muscle hypertrophy in pre-menopausal females. In vivo nuclear localisation of the androgen receptor was positively related to muscle mass in pre-menopausal females at baseline, but not to resistance training-induced hypertrophy. Testosterone treatment induced androgen receptor nuclear translocation but did not induce mTOR signalling in primary skeletal myocytes cultured from pre-menopausal female muscle.
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Affiliation(s)
- Sarah E Alexander
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
- Cardiometabolic Health and Exercise Physiology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Briana Gatto
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Olivia E Knowles
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Ross M Williams
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Kinga N Fiebig
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Paul Jansons
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Paul A Della Gatta
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Andrew Garnham
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Nir Eynon
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Glenn D Wadley
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Brad Aisbett
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Danielle Hiam
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
| | - Séverine Lamon
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Victoria, Australia
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176
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Gopakumar G, Diaz-Méndez A, Coppo MJC, Hartley CA, Devlin JM. Transcriptomic analyses of host-virus interactions during in vitro infection with wild-type and glycoprotein g-deficient (ΔgG) strains of ILTV in primary and continuous cell cultures. PLoS One 2024; 19:e0311874. [PMID: 39392810 PMCID: PMC11469545 DOI: 10.1371/journal.pone.0311874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 09/25/2024] [Indexed: 10/13/2024] Open
Abstract
Infectious laryngotracheitis (ILT) remains a significant concern for the poultry industry worldwide due to its impact on animal welfare and its substantial economic consequences. The disease is caused by the alphaherpesvirus, infectious laryngotracheitis virus (ILTV). This study investigated in vitro host-virus interactions of a glycoprotein G (gG) deletion mutant vaccine strain of ILTV (ΔgG ILTV), and its parent wild-type strain (CSW-1 ILTV). Inoculations were performed separately for the two strains of ILTV using both a primary (chicken embryonic kidney, CEK) and a continuous culture (leghorn male hepatoma, LMH) of chicken cells. Transcriptome analysis was performed at 12 hours post infection. Each cell-type displayed distinct effects on host and viral gene transcription, with a greater number of viral and host genes differentially transcribed in CEK cells and LMH cells, respectively. Both cell-types infected with either strain demonstrated enrichment of pathways related to signalling, and gene ontologies (GO) associated with chemotaxis. Infection with either strain upregulated both SOCS proteins and certain proto-oncogenes, which may contribute to prolonged viral persistence by promoting immunosuppression and preventing apoptosis, respectively. Patterns of gene transcription related to cytokines, chemokines, endosomal TLRs, and interferon responses, as well as pathways associated with histone acetylation, transport, and extracellular matrix organization were similar within each cell type, regardless of the viral strain. In CEK cells, GO terms and pathways were downregulated uniquely after CSW-1 ILTV infection, indicating a viral-strain specific effect in this cell-type. Overall, this study highlights that the observed differences in host and ILTV gene transcription in vitro were more strongly influenced by the cell-types used rather than the presence or absence of gG. This underscores the importance of cell-line selection in studying host-virus interactions and interpreting experimental results.
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Affiliation(s)
- Gayathri Gopakumar
- Faculty of Science, Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Andrés Diaz-Méndez
- Faculty of Science, Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mauricio J. C. Coppo
- Faculty of Science, Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
- Escuela de Medicina Veterinaria, Universidad Andrés Bello, Concepción, Biobío, Chile
| | - Carol A. Hartley
- Faculty of Science, Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Joanne M. Devlin
- Faculty of Science, Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
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Burattin FV, Vadalà R, Panepuccia M, Ranzani V, Crosti M, Colombo FA, Ruberti C, Erba E, Prati D, Nittoli T, Montini G, Ronchi A, Pugni L, Mosca F, Ricciardi S, Abrignani S, Pietrasanta C, Marasca F, Bodega B. LINE1 modulate human T cell function by regulating protein synthesis during the life span. SCIENCE ADVANCES 2024; 10:eado2134. [PMID: 39383231 PMCID: PMC11463280 DOI: 10.1126/sciadv.ado2134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 09/04/2024] [Indexed: 10/11/2024]
Abstract
The molecular mechanisms responsible for the heightened reactivity of quiescent T cells in human early life remain largely elusive. Our previous research identified that quiescent adult naïve CD4+ T cells express LINE1 (long interspersed nuclear elements 1) spliced in previously unknown isoforms, and their down-regulation marks the transition to activation. Here, we unveil that neonatal naïve T cell quiescence is characterized by enhanced energy production and protein synthesis. This phenotype is associated with the absence of LINE1 expression attributed to tonic T cell receptor/mTOR complex 1 (mTORC1) signaling and (polypyrimidine tract-binding protein 1 (PTBP1)-mediated LINE1 splicing suppression. The absence of LINE1 expression primes these cells for rapid execution of the activation program by directly regulating protein synthesis. LINE1 expression progressively increases in childhood and adults, peaking in elderly individuals, and, by decreasing protein synthesis, contributes to immune senescence in aging. Our study proposes LINE1 as a critical player of human T cell function across the human life span.
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Affiliation(s)
- Filippo V. Burattin
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Milan 20122, Italy
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Rebecca Vadalà
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Michele Panepuccia
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Milan 20122, Italy
- SEMM, European School of Molecular Medicine, Milan 20139, Italy
| | - Valeria Ranzani
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Milan 20122, Italy
| | - Mariacristina Crosti
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Milan 20122, Italy
| | - Federico A. Colombo
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Milan 20122, Italy
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Cristina Ruberti
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Elisa Erba
- Department of Transfusion Medicine and Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Teresa Nittoli
- Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Giovanni Montini
- Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Andrea Ronchi
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Lorenza Pugni
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Fabio Mosca
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Sara Ricciardi
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Milan 20122, Italy
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Sergio Abrignani
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Milan 20122, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Carlo Pietrasanta
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
- Neonatal Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Federica Marasca
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Milan 20122, Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Milan 20122, Italy
- Department of Biosciences, University of Milan, Milan 20133, Italy
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Teo AYY, Squair JW, Courtine G, Skinnider MA. Best practices for differential accessibility analysis in single-cell epigenomics. Nat Commun 2024; 15:8805. [PMID: 39394227 PMCID: PMC11470024 DOI: 10.1038/s41467-024-53089-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/24/2024] [Indexed: 10/13/2024] Open
Abstract
Differential accessibility (DA) analysis of single-cell epigenomics data enables the discovery of regulatory programs that establish cell type identity and steer responses to physiological and pathophysiological perturbations. While many statistical methods to identify DA regions have been developed, the principles that determine the performance of these methods remain unclear. As a result, there is no consensus on the most appropriate statistical methods for DA analysis of single-cell epigenomics data. Here, we present a systematic evaluation of statistical methods that have been applied to identify DA regions in single-cell ATAC-seq (scATAC-seq) data. We leverage a compendium of scATAC-seq experiments with matching bulk ATAC-seq or scRNA-seq in order to assess the accuracy, bias, robustness, and scalability of each statistical method. The structure of our experiments also provides the opportunity to define best practices for the analysis of scATAC-seq data beyond DA itself. We leverage this understanding to develop an R package implementing these best practices.
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Affiliation(s)
- Alan Yue Yang Teo
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland
- NeuroX Institute and Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Jordan W Squair
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland.
- NeuroX Institute and Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Gregoire Courtine
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland.
- NeuroX Institute and Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Michael A Skinnider
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland.
- NeuroX Institute and Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA.
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Pietsch N, Chen CY, Kupsch S, Bacmeister L, Geertz B, Herrera-Rivero M, Siebels B, Voß H, Krämer E, Braren I, Westermann D, Schlüter H, Mearini G, Schlossarek S, van der Velden J, Caporizzo MA, Lindner D, Prosser BL, Carrier L. Chronic Activation of Tubulin Tyrosination Improves Heart Function. Circ Res 2024; 135:910-932. [PMID: 39279670 PMCID: PMC11465905 DOI: 10.1161/circresaha.124.324387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/18/2024]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is the most common cardiac genetic disorder caused by sarcomeric gene variants and associated with left ventricular hypertrophy and diastolic dysfunction. The role of the microtubule network has recently gained interest with the findings that microtubule detyrosination (dTyr-MT) is markedly elevated in heart failure. Acute reduction of dTyr-MT by inhibition of the detyrosinase (VASH [vasohibin]/SVBP [small VASH-binding protein] complex) or activation of the tyrosinase (TTL [tubulin tyrosine ligase]) markedly improved contractility and reduced stiffness in human failing cardiomyocytes and thus posed a new perspective for HCM treatment. In this study, we tested the impact of chronic tubulin tyrosination in an HCM mouse model (Mybpc3 knock-in), in human HCM cardiomyocytes, and in SVBP-deficient human engineered heart tissues (EHTs). METHODS Adeno-associated virus serotype 9-mediated TTL transfer was applied in neonatal wild-type rodents, in 3-week-old knock-in mice, and in HCM human induced pluripotent stem cell-derived cardiomyocytes. RESULTS We show (1) TTL for 6 weeks dose dependently reduced dTyr-MT and improved contractility without affecting cytosolic calcium transients in wild-type cardiomyocytes; (2) TTL for 12 weeks reduced the abundance of dTyr-MT in the myocardium, improved diastolic filling, compliance, cardiac output, and stroke volume in knock-in mice; (3) TTL for 10 days normalized cell area in HCM human induced pluripotent stem cell-derived cardiomyocytes; (4) TTL overexpression activated transcription of tubulins and other cytoskeleton components but did not significantly impact the proteome in knock-in mice; (5) SVBP-deficient EHTs exhibited reduced dTyr-MT levels, higher force, and faster relaxation than TTL-deficient and wild-type EHTs. RNA sequencing and mass spectrometry analysis revealed distinct enrichment of cardiomyocyte components and pathways in SVBP-deficient versus TTL-deficient EHTs. CONCLUSIONS This study provides the first proof of concept that chronic activation of tubulin tyrosination in HCM mice and in human EHTs improves heart function and holds promise for targeting the nonsarcomeric cytoskeleton in heart disease.
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Affiliation(s)
- Niels Pietsch
- Department of Experimental Pharmacology and Toxicology (N.P., B.G., E.K., G.M., S.S., L.C.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Germany (N.P., D.W., G.M., S.S., D.L., L.C.)
| | - Christina Y. Chen
- Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (C.Y.C., M.A.C., B.L.P.)
- Now with Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA (C.Y.C.)
| | - Svenja Kupsch
- Department of Cardiology, University Heart and Vascular Center (S.K., L.B., D.W., D.L.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Now with Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Germany (S.K.)
| | - Lucas Bacmeister
- Department of Cardiology, University Heart and Vascular Center (S.K., L.B., D.W., D.L.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Now with Faculty of Medicine, Department of Cardiology and Angiology, University Heart Center Freiburg-Bad Krozingen, University of Freiburg, Germany (L.B., D.W., D.L.)
| | - Birgit Geertz
- Department of Experimental Pharmacology and Toxicology (N.P., B.G., E.K., G.M., S.S., L.C.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marisol Herrera-Rivero
- Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Germany (M.H.-R.)
- Joint Institute for Individualisation in a Changing Environment, University of Münster and Bielefeld University, Münster, Germany (M.H.-R.)
| | - Bente Siebels
- Section Mass Spectrometric Proteomics (B.S., H.V., H.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section Mass Spectrometric Proteomics (B.S., H.V., H.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elisabeth Krämer
- Department of Experimental Pharmacology and Toxicology (N.P., B.G., E.K., G.M., S.S., L.C.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ingke Braren
- Vector Facility, Department of Experimental Pharmacology and Toxicology (I.B.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dirk Westermann
- Department of Cardiology, University Heart and Vascular Center (S.K., L.B., D.W., D.L.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Now with Faculty of Medicine, Department of Cardiology and Angiology, University Heart Center Freiburg-Bad Krozingen, University of Freiburg, Germany (L.B., D.W., D.L.)
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Germany (N.P., D.W., G.M., S.S., D.L., L.C.)
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics (B.S., H.V., H.S.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Giulia Mearini
- Department of Experimental Pharmacology and Toxicology (N.P., B.G., E.K., G.M., S.S., L.C.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Germany (N.P., D.W., G.M., S.S., D.L., L.C.)
| | - Saskia Schlossarek
- Department of Experimental Pharmacology and Toxicology (N.P., B.G., E.K., G.M., S.S., L.C.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Germany (N.P., D.W., G.M., S.S., D.L., L.C.)
| | - Jolanda van der Velden
- Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands (J.v.d.V.)
| | - Matthew A. Caporizzo
- Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (C.Y.C., M.A.C., B.L.P.)
- Now with Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT (M.A.C.)
| | - Diana Lindner
- Department of Cardiology, University Heart and Vascular Center (S.K., L.B., D.W., D.L.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Now with Faculty of Medicine, Department of Cardiology and Angiology, University Heart Center Freiburg-Bad Krozingen, University of Freiburg, Germany (L.B., D.W., D.L.)
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Germany (N.P., D.W., G.M., S.S., D.L., L.C.)
| | - Benjamin L. Prosser
- Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (C.Y.C., M.A.C., B.L.P.)
| | - Lucie Carrier
- Department of Experimental Pharmacology and Toxicology (N.P., B.G., E.K., G.M., S.S., L.C.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Germany (N.P., D.W., G.M., S.S., D.L., L.C.)
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Easterling KA, Marshall AT, Pitino M, Walker WB, Cooper WR. Gene expression profiling of Cacopsylla pyricola (Hemiptera: Psyllidae) infected with Ca. Phytoplasma pyri (Acholeplasmatales: Acholeplasmataceae) reveals candidate effectors and mechanisms of infection. ENVIRONMENTAL ENTOMOLOGY 2024; 53:771-781. [PMID: 39235989 DOI: 10.1093/ee/nvae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/31/2024] [Accepted: 08/20/2024] [Indexed: 09/07/2024]
Abstract
Phytoplasmas can negatively or positively alter vector host fitness. "Candidatus Phytoplasma pyri," is the causal agent of pear decline in commercial pear (Pyrus communis L.; Rosales: Rosaceae) and peach yellow leafroll in peach [Prunus persica (L.); Rosaceae]. This plant pathogen is transmitted by several species of pear psyllids (Cacopsylla spp. Hemiptera: Psyllidae). We sought to explore the relationship between the pear decline phytoplasma and its US vector, Cacopsylla pyricola (Förster), at the molecular genetic level through transcriptomic analysis using RNA-sequencing methodology. We also focused on phytoplasma and insect effectors, which are secreted proteins that can modulate interactions within a pathosystem. In this study, we identified 30 differentially expressed genes, 14 candidate insect effector genes, and 8 Ca. Phytoplasma pyri candidate effectors. Two strains of Ca. Phytoplasma pyri were identified based on immunodominant membrane protein sequence analysis from C. pyricola collected in the Pacific Northwest agricultural region. Here, we present a first genetic look at the pear decline pathosystem and report gene candidates for further exploration of infection mechanisms and potential tools for integrated pest management.
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Affiliation(s)
| | - Adrian T Marshall
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, Wapato, WA, USA
| | - Marco Pitino
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, Wapato, WA, USA
| | - William B Walker
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, Wapato, WA, USA
| | - W Rodney Cooper
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, Wapato, WA, USA
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181
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Hu R, Chen F, Yu X, Li Z, Li Y, Feng S, Liu J, Li H, Shen C, Gu X, Lu Z. Construction and validation of a prognostic model of angiogenesis-related genes in multiple myeloma. BMC Cancer 2024; 24:1269. [PMID: 39394121 PMCID: PMC11470605 DOI: 10.1186/s12885-024-13024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 10/03/2024] [Indexed: 10/13/2024] Open
Abstract
BACKGROUND Angiogenesis is associated with tumour growth, infiltration, and metastasis. This study aimed to detect the mechanisms of angiogenesis-related genes (ARGs) in multiple myeloma (MM) and to construct a new prognostic model. METHODS MM research foundation (MMRF)-CoMMpass cohort, GSE47552, GSE57317, and ARGs were sourced from public databases. Differentially expressed genes (DEGs) in the tumour and control cohorts in GSE47552 were determined through differential expression analysis and were enriched with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Weighted gene coexpression network analysis (WGCNA) was applied to derive modules linked to the ARG scores and obtain module genes in GSE47552. Differentially expressed ARGs (DE-ARGs) were selected for subsequent analyses by overlapping DEGs and module genes. Furthermore, prognostic genes were selected using univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses. Depending on the prognostic genes, a risk model was constructed, and risk scores were determined. Moreover, MM samples from MMRF-CoMMpass were sorted into high- and low-risk teams on account of the median risk score. Additionally, correlations among clinical characteristics, gene set variation analysis (GSVA), gene set enrichment analysis (GSEA), immune analysis, immunotherapy predictions and the mRNA‒miRNA‒lncRNA network were carried out. RESULTS A total of 898 DEGs, 211 module genes, 24 DE-ARGs and three prognostic genes (AKAP12, C11orf80 and EMP1) were selected for this study. Enrichment analysis revealed that the DEGs were related to 86 GO terms, such as 'cytoplasmic translation', and 41 KEGG pathways, such as 'small cell lung cancer'. A prognostic gene-based risk model was created in MMRF-CoMMpass and confirmed with the GSE57317 dataset. Moreover, a nomogram was established on the basis of independent prognostic factors that have proven to be good predictors. In addition, the immune cell infiltration results suggested that memory B cells were enriched in the high-risk group and that immature B cells were enriched in the low-risk group. Finally, the mRNA‒miRNA‒lncRNA network demonstrated that hsa-miR-508-5p was tightly associated with EMP1 and AKAP12. RT‒qPCR was used to validate the expression of the genes associated with prognosis. CONCLUSION A new prognostic model of MM associated with ARGs was created and validated, providing a new perspective for exploring the connection between ARGs and MM.
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Affiliation(s)
- Rui Hu
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China
| | - Fengyu Chen
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China
| | - Xueting Yu
- Department of Endocrinology, 920th Hospital of Joint Logistics Support Force,PLA, Kunming, China
| | - Zengzheng Li
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China
| | - Yujin Li
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China
| | - Shuai Feng
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China
| | - Jianqiong Liu
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China
| | - Huiyuan Li
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China
| | - Chengmin Shen
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China
| | - Xuezhong Gu
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China.
| | - Zhixiang Lu
- Department of Hematology, The First People's Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Hu Yu Expert Workstation, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Yunnan Provincial Clinical Medical Center for Blood Diseases and Thrombosis Prevention and Treatment, Kunming, Yunnan, China
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Jiang M, Sun J, Hu C, Wu L, Fan Y, Wang Z, Liu L, Wu C, Wu F, Gao G, Li F, Wang L, Li X, Cheng L, Peng B, Zhou H, Zhou C. A tumor cornification and immune-infiltration-based scheme for anti-PD-1 plus chemotherapy response in advanced squamous cell lung carcinoma. MED 2024:S2666-6340(24)00372-6. [PMID: 39395411 DOI: 10.1016/j.medj.2024.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 07/29/2024] [Accepted: 09/13/2024] [Indexed: 10/14/2024]
Abstract
BACKGROUND Anti-PD-1 immunotherapy plus chemotherapy (combo) exhibits significantly prolonged survival for squamous cell lung cancer (LUSC). An exploration of predictive biomarkers is still needed. METHODS High-throughput RNA sequencing (RNA-seq) of 349 LUSC samples from the randomized, multi-center, phase 3 trial ORIENT-12 (ClinicalTrials.gov: NCT03629925) was conducted for biomarker discovery, followed by flow cytometry and multiplex immunohistochemistry (mIHC) in additional clinical cohorts, and in vitro experiments were performed for verification. RESULTS A high abundance of activated CD8+ T and CD56bright natural killer (NK) cells benefited patients' outcomes (progression-free survival [PFS]; overall survival [OS]) with combo treatment. Tumor cornification level remarkably affected the infiltration of the two crucial immune cells. Thus, a novel scheme of LUSC immune infiltration and cornification characterization-based classification (LICC) was established for combo efficacy prediction. Patients who received combo treatment achieved significant PFS improvements in LICC1 (hazard ratio [HR] = 0.43, 95% confidence interval [CI]: 0.25-0.75, p = 0.0029) and LICC2 (HR = 0.32, 95% CI: 0.17-0.58, p = 0.0002) subtypes but not in the LICC3 subtype (HR = 0.86, 95% CI: 0.60-1.23, p = 0.4053). Via single-cell RNA-seq analysis, the tumor cornification signal was mainly mapped to SPRR3+ tumor cells, whose relationships with activated CD8+ T or CD56bright NK cells were verified using flow cytometry and mIHC. Our data suggest that SPRR3+ tumor cells might evade immune surveillance via the CD24-SIGLEC10 (M2 macrophage) axis to maintain a suppressive tumor microenvironment. CONCLUSIONS Tumor cornification greatly impacts immune infiltration, and the LICC scheme may guide clinical medication of anti-PD-1+chemo treatment in patients with LUSC. FUNDING The study was funded by the National Key R&D Program of China, the National Natural Science Foundation of China, Shanghia Multidisplinary Cooperation Building Project for Diagnosis and Treatment of Major Disease, and Innovent Biologics, Inc.
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Affiliation(s)
- Minlin Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China; Medical School, Tongji University, Shanghai 200433, China
| | - Jiya Sun
- Innovent Biologics, Inc., Suzhou, Jiangsu 215123, China
| | - Congli Hu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China; Medical School, Tongji University, Shanghai 200433, China
| | - Lin Wu
- Thoracic Medicine Department II, Hunan Cancer Hospital, Changsha, Hunan 410031, China
| | - Yun Fan
- Oncology Department, Cancer Hospital of the University of Chinese Academy of Science, Hangzhou, Zhejiang 310005, China
| | - Zhehai Wang
- Respiratory Department, Shandong Cancer Hospital, Jinan, Shandong 250117, China
| | - Lianke Liu
- Oncology Department, Jiangsu Province Hospital, Nanjing, Jiangsu 210029, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai 200433, China
| | - Fengying Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Guanghui Gao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Fei Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Frontier Innovation Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Xuefei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Lei Cheng
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Bo Peng
- Innovent Biologics, Inc., Suzhou, Jiangsu 215123, China
| | - Hui Zhou
- Innovent Biologics, Inc., Suzhou, Jiangsu 215123, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai East Hospital, Shanghai 200120, China.
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183
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Ge T, Gui X, Xu JX, Xia W, Wang CH, Yang W, Huang K, Walsh C, Umen JG, Walter J, Du YR, Chen H, Shao Z, Xu GL. DNA cytosine methylation suppresses meiotic recombination at the sex-determining region. SCIENCE ADVANCES 2024; 10:eadr2345. [PMID: 39383224 PMCID: PMC11463267 DOI: 10.1126/sciadv.adr2345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 09/04/2024] [Indexed: 10/11/2024]
Abstract
Meiotic recombination between homologous chromosomes is vital for maximizing genetic variation among offspring. However, sex-determining regions are often rearranged and blocked from recombination. It remains unclear whether rearrangements or other mechanisms might be responsible for recombination suppression. Here, we uncover that the deficiency of the DNA cytosine methyltransferase DNMT1 in the green alga Chlamydomonas reinhardtii causes anomalous meiotic recombination at the mating-type locus (MT), generating haploid progeny containing both plus and minus mating-type markers due to crossovers within MT. The deficiency of a histone methyltransferase for H3K9 methylation does not lead to anomalous recombination. These findings suggest that DNA methylation, rather than rearrangements or histone methylation, suppresses meiotic recombination, revealing an unappreciated biological function for DNA methylation in eukaryotes.
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Affiliation(s)
- Tong Ge
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiuqi Gui
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Xi Xu
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Xia
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao-Han Wang
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenqiang Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Colum Walsh
- Department of Cell Biology, Institute for Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - James G. Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO 63132, USA
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken 66123, Germany
| | - Ya-Rui Du
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Chen
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen Shao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Liang Xu
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Chinese Academy of Medical Sciences (RU069) and Zhongshan-Xuhui Hospital, Fudan University, Shanghai 200032, China
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Ren J, Wang Y, Zhang Y, Jin H, Cheng J, Tao F, Zhu Y. Placental Transcriptomic Signatures of Prenatal Phthalate Exposure and Identification of Placenta-Brain Genes Associated with the Effects of Phthalate Exposure on Neurodevelopment in Children. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39392919 DOI: 10.1021/acs.est.4c04082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2024]
Abstract
Prenatal exposure to phthalates may affect placental function and fetal development, but the underlying mechanisms are unclear. The aim of our study was to explore the alterations in the placental transcriptome associated with prenatal phthalate exposure and to further analyze whether the placental-brain axis (PBA) genes play a mediating role in the association between prenatal phthalate exposure and children's neurodevelopment. We included 172 participants from the Ma'anshan Birth Cohort and collected data on seven phthalate metabolites in urine during pregnancy, placental tissue RNA-seq, and neurodevelopment of offspring. Bioinformatics analysis revealed that aberrant regulation of the placental transcriptome was associated with prenatal phthalate exposure. Exposure to phthalates during pregnancy was found to be associated with neurodevelopmental delay in children aged 6, 18, and 48 months using the multiple linear regression model. Meanwhile, employing mediation analysis, nine PBA genes were identified that mediate the association between exposure to phthalates during pregnancy and the neurodevelopment of children. Our study will provide a basis for potential mechanisms by which prenatal exposure to phthalates affects placental function and children's neurodevelopment.
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Affiliation(s)
- Jiawen Ren
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei 230032, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Environment and Population Health across the Life Course, Anhui Medical University, Hefei 230032, Anhui, China
| | - Yifan Wang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei 230032, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Environment and Population Health across the Life Course, Anhui Medical University, Hefei 230032, Anhui, China
| | - Yimin Zhang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei 230032, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Environment and Population Health across the Life Course, Anhui Medical University, Hefei 230032, Anhui, China
| | - Heyue Jin
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei 230032, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Environment and Population Health across the Life Course, Anhui Medical University, Hefei 230032, Anhui, China
| | - Jingjing Cheng
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei 230032, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Environment and Population Health across the Life Course, Anhui Medical University, Hefei 230032, Anhui, China
| | - Fangbiao Tao
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei 230032, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Environment and Population Health across the Life Course, Anhui Medical University, Hefei 230032, Anhui, China
| | - Yumin Zhu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei 230032, Anhui, China
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Environment and Population Health across the Life Course, Anhui Medical University, Hefei 230032, Anhui, China
- Medical School, Nanjing University, Nanjing 210093, Jiangsu, China
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185
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Liu T, Shen X, Ren Y, Lu H, Liu Y, Chen C, Yu L, Xue Z. Genome-wide mapping of native co-localized G4s and R-loops in living cells. eLife 2024; 13:RP99026. [PMID: 39392462 PMCID: PMC11469684 DOI: 10.7554/elife.99026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024] Open
Abstract
The interplay between G4s and R-loops are emerging in regulating DNA repair, replication, and transcription. A comprehensive picture of native co-localized G4s and R-loops in living cells is currently lacking. Here, we describe the development of HepG4-seq and an optimized HBD-seq methods, which robustly capture native G4s and R-loops, respectively, in living cells. We successfully employed these methods to establish comprehensive maps of native co-localized G4s and R-loops in human HEK293 cells and mouse embryonic stem cells (mESCs). We discovered that co-localized G4s and R-loops are dynamically altered in a cell type-dependent manner and are largely localized at active promoters and enhancers of transcriptional active genes. We further demonstrated the helicase Dhx9 as a direct and major regulator that modulates the formation and resolution of co-localized G4s and R-loops. Depletion of Dhx9 impaired the self-renewal and differentiation capacities of mESCs by altering the transcription of co-localized G4s and R-loops -associated genes. Taken together, our work established that the endogenous co-localized G4s and R-loops are prevalently persisted in the regulatory regions of active genes and are involved in the transcriptional regulation of their linked genes, opening the door for exploring broader roles of co-localized G4s and R-loops in development and disease.
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Affiliation(s)
- Ting Liu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Xing Shen
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Yijia Ren
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Hongyu Lu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Yu Liu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan UniversityChengduChina
| | - Chong Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan UniversityChengduChina
| | - Lin Yu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Zhihong Xue
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan ProvinceChengduChina
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186
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Bergström B, Selldén T, Bollmann M, Svensson MND, Ekwall AKH. Methotrexate promotes the release of granulocyte-macrophage colony-stimulating factor from rheumatoid arthritis fibroblast-like synoviocytes via autocrine interleukin-1 signaling. Arthritis Res Ther 2024; 26:178. [PMID: 39394168 PMCID: PMC11468154 DOI: 10.1186/s13075-024-03406-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 09/23/2024] [Indexed: 10/13/2024] Open
Abstract
BACKGROUND Activated fibroblast-like synoviocytes (FLS) are drivers of synovitis and structural joint damage in rheumatoid arthritis (RA). Despite the use of disease-modifying drugs, only about 50% of RA patients reach remission in real-world settings. We used an unbiased approach to investigate the effects of standard-of-care methotrexate (MTX) and a Janus kinase inhibitor, tofacitinib (TOFA), on gene expression in RA-FLS, in order to identify untargeted disease mediators. METHODS Primary RA-FLS were activated by stimulation with interleukin-1β (IL-1β) or platelet-derived growth factor + IL-1β in the presence or absence of MTX or TOFA, with or without additional inhibitors. Co-cultures of synovial cells were performed in direct and indirect systems. Cells were collected for RNA sequencing or qPCR, and supernatants were analyzed for protein concentrations. RESULTS Six thousand three hundred fifty genes were differentially expressed, the majority being upregulated, in MTX-treated activated RA-FLS and 970 genes, the majority being downregulated, in TOFA-treated samples. Pathway analysis showed that MTX had largest effects on 'Molecular mechanisms of cancer' and TOFA on 'Interferon signaling'. Targeted analysis of disease-associated genes revealed that MTX increased the expression of cell cycle-regulating genes but also of pro-inflammatory mediators like IL-1α (IL1A) and granulocyte-macrophage colony-stimulating factor, GM-CSF (CSF2). The MTX-promoted expression of CSF2 in activated RA-FLS peaked at 48 h, could be mediated via either NF-κB or AP-1 transcription factors, and was abrogated by IL-1 inhibitors (IRAK4 inhibitor and anakinra). In a co-culture setting, MTX-treatment of activated RA-FLS induced IL1B expression in macrophages. CONCLUSIONS MTX treatment induces secretion of IL-1 from activated RA-FLS which by autocrine signaling augments their release of GM-CSF. This unexpected effect of MTX might contribute to the persistence of synovitis.
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Affiliation(s)
- Beatrice Bergström
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tilia Selldén
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Miriam Bollmann
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- SciLifeLab, University of Gothenburg, Gothenburg, Sweden
| | - Mattias N D Svensson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- SciLifeLab, University of Gothenburg, Gothenburg, Sweden
| | - Anna-Karin Hultgård Ekwall
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Department of Rheumatology, Division 3, Sahlgrenska University Hospital, Gothenburg, Sweden.
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187
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Weinstock JS, Arce MM, Freimer JW, Ota M, Marson A, Battle A, Pritchard JK. Gene regulatory network inference from CRISPR perturbations in primary CD4 + T cells elucidates the genomic basis of immune disease. CELL GENOMICS 2024:100671. [PMID: 39395408 DOI: 10.1016/j.xgen.2024.100671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 06/04/2024] [Accepted: 09/16/2024] [Indexed: 10/14/2024]
Abstract
The effects of genetic variation on complex traits act mainly through changes in gene regulation. Although many genetic variants have been linked to target genes in cis, the trans-regulatory cascade mediating their effects remains largely uncharacterized. Mapping trans-regulators based on natural genetic variation has been challenging due to small effects, but experimental perturbations offer a complementary approach. Using CRISPR, we knocked out 84 genes in primary CD4+ T cells, targeting inborn error of immunity (IEI) disease transcription factors (TFs) and TFs without immune disease association. We developed a novel gene network inference method called linear latent causal Bayes (LLCB) to estimate the network from perturbation data and observed 211 regulatory connections between genes. We characterized programs affected by the TFs, which we associated with immune genome-wide association study (GWAS) genes, finding that JAK-STAT family members are regulated by KMT2A, an epigenetic regulator. These analyses reveal the trans-regulatory cascades linking GWAS genes to signaling pathways.
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Affiliation(s)
- Joshua S Weinstock
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Maya M Arce
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jacob W Freimer
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Mineto Ota
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94129, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA, USA.
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188
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He Q, Zhang Y, Li W, Chen S, Xiong J, Zhao R, Yuan K, Hu Q, Liu S, Gao G, Bedford MT, Tang DG, Xu B, Zou C, Zhang D. Inhibition of PRMT5 moderately suppresses prostate cancer growth in vivo but enhances its response to immunotherapy. Cancer Lett 2024; 602:217214. [PMID: 39218291 DOI: 10.1016/j.canlet.2024.217214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/11/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Protein arginine methylation is a common post-translational modification (PTM) catalyzed by nine protein arginine methyltransferases (PRMTs). As the major symmetric arginine methyltransferase that methylates both histone and non-histone substrates, PRMT5 plays key roles in a number of biological processes critical for development and tumorigenesis. PRMT5 overexpression has been reported in multiple cancer types including prostate cancer (PCa), but the exact biological and mechanistic understanding of PRMT5 in aggressive PCa remains ill-defined. Here, we show that PRMT5 is upregulated in PCa, correlates with worse patient survival, promotes corrupted RNA splicing, and functionally cooperates with an array of pro-tumorigenic pathways to enhance oncogenesis. PRMT5 inhibition via either genetic knockdown or pharmacological inhibition reduces stemness with paralleled differentiation and arrests cell cycle progression without causing appreciable apoptosis. Strikingly, the severity of antitumor effect of PRMT5 inhibition correlates with disease aggressiveness, with AR+ PCa being less affected. Molecular characterization pinpoints MYC, but not (or at least to a lesser degree) AR, as the main partner of PRMT5 to form a positive feedback loop to exacerbate malignancy in both AR+ and AR- PCa cells. Inspired by the surprising finding that PRMT5 negatively correlates with tumor immune infiltration and transcriptionally suppresses an immune-gene program, we further show that although PRMT5 inhibitor (PRMT5i) EPZ015666 or anti-PD-1 immunotherapy alone exhibits limited antitumor effects, combination of PRMT5i with anti-PD-1 displays superior efficacy in inhibiting castration-resistant PCa (CRPC) in vivo. Finally, to expand the potential use of PRMT5i through a synthetic lethality concept, we also perform a global CRISPR/Cas9 knockout screen to unravel that many clinical-grade drugs of known oncogenic pathways can be repurposed to target CRPC when used in combination with PRMT5i at low doses. Collectively, our findings establish a rationale to exploit PRMT5i in combination with immunotherapy or other targeted therapies to treat aggressive PCa.
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Affiliation(s)
- Qinju He
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Yuanzhen Zhang
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Saisai Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Jiangling Xiong
- Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Ruizhe Zhao
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA; Current Address: Department of Urology, First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410000, China
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, 14263, New York, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, 14263, New York, USA
| | - Guozhen Gao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dean G Tang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China.
| | - Cheng Zou
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China; Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China.
| | - Dingxiao Zhang
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Key Laboratory of Animal Models and Molecular Medicine, Hunan University, Changsha, 410082, China; Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China.
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Xu Y, Yan Y, Zhou T, Lu Y, Yang X, Tang K, Liu F. Synergy between Arbuscular Mycorrhizal Fungi and Rhizosphere Bacterial Communities Increases the Utilization of Insoluble Phosphorus and Potassium in the Soil by Maize. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39389770 DOI: 10.1021/acs.jafc.4c07428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Arbuscular mycorrhizal (AM) fungi can enhance plant uptake of phosphorus (P) and potassium (K), but it is not yet clear whether rhizosphere bacteria can enhance the ability of AM fungi to acquire insoluble P and K from the soil. Here, pot experiments confirmed that AM fungus-promoted insoluble P and K uptake by plants requires rhizosphere bacteria. The changes of rhizosphere bacterial communities associated with AM fungi were explored by 16S rRNA amplicon sequencing and metagenomic sequencing. Five core bacteria genera identified were involved in P and K cycles. Synthetic community (SynCom) inoculation revealed that SynCom increased soil available P and K and its coinoculation with AM fungi increased P and K concentration in the plants. This study revealed that AM fungi interact with rhizosphere bacteria and promote insoluble P and K acquisition, which provided a foundation for the application of AM fungal-bacterial biofertilizers and was beneficial for the sustainable development of agriculture.
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Affiliation(s)
- Yunjian Xu
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan 650504, China
| | - Yixiu Yan
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Tianyi Zhou
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Yufan Lu
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Xinyu Yang
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Kailei Tang
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Fang Liu
- School of Agriculture, Yunnan University, Kunming 650504, China
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190
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Yan W, Zhu Y, Zou C, Liu W, Jia B, Niu J, Zhou Y, Chen B, Li R, Ding SW, Wu Q, Guo Z. Virome Characterization of Native Wild-Rice Plants Discovers a Novel Pathogenic Rice Polerovirus With World-Wide Circulation. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39390751 DOI: 10.1111/pce.15204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/09/2024] [Accepted: 09/29/2024] [Indexed: 10/12/2024]
Abstract
Pandemics originating from zoonotic viruses have posed significant threats to human health and agriculture. Recent discoveries have revealed that wild-rice plants also harbour viral pathogens capable of severely impacting rice production, a cornerstone food crop. In this study, we conducted virome analysis on ~1000 wild-rice individual colonies and discovered a novel single-strand positive-sense RNA virus prevalent in these plants. Through comprehensive genomic characterization and comparative sequence analysis, this virus was classified as a new species in the genus Polerovirus, designated Rice less tiller virus (RLTV). Our investigations elucidated that RLTV could be transmitted from wild rice to cultivated rice via a specific insect vector, the aphid Rhopalosiphum padi, causing less tiller disease symptoms in rice plants. We generated an infectious cDNA clone for RLTV and demonstrated systemic infection of rice cultivars and induction of severe disease symptoms following mechanical inoculation or stable genetic transformation. We further illustrated transmission of RLTV from stable transgenic lines to healthy rice plants by the aphid vector, leading to the development of disease symptoms. Notably, our database searches showed that RLTV and another polerovirus isolated from a wild plant species are widely circulating not only in wild rice but also cultivated rice around the world. Our findings provide strong evidence for a wild plant origin for rice viruses and underscore the imminent threat posed by aphid-transmitted rice Polerovirus to rice cultivar.
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Affiliation(s)
- Wenkai Yan
- Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chengwu Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Wencheng Liu
- Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bei Jia
- Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiangshuai Niu
- Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yaogui Zhou
- Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory for Microbial and Plant Genetic Engineering, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Shou-Wei Ding
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhongxin Guo
- Vector-borne Virus Research Center, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
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191
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Li A, Wang X, Li J, Li X, Wang J, Liu Y, Wang Z, Yang X, Gao J, Wu J, Sun T, Huo L, Yi Y, Shen J, Cai J, Yao Y. Critical role of G protein-coupled receptor 40 in B cell response and the pathogenesis of rheumatoid arthritis in mice and patients. Cell Rep 2024; 43:114858. [PMID: 39392754 DOI: 10.1016/j.celrep.2024.114858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/06/2024] [Accepted: 09/25/2024] [Indexed: 10/13/2024] Open
Abstract
Rheumatoid arthritis (RA) is marked by joint damage and inflammation, with B cells playing a key role by generating autoantibodies. This study shows that G protein-coupled receptor 40 (GPR40) deficiency in B cells leads to increased activation, proliferation, antibody production, germinal center formation, and class switch recombination. GPR40 regulates Plcγ2 phosphorylation and intracellular calcium flux downstream of the B cell receptor by binding to the Gαq protein. In GPR40-deficient mice, susceptibility to collagen-induced arthritis was higher. GPR40 agonists showed potential as therapeutic agents, and their reduced expression in patients with RA correlated with disease onset, suggesting GPR40 as a potential therapeutic target and diagnostic marker.
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Affiliation(s)
- Anqi Li
- School of Medicine & Nursing, Huzhou University, Huzhou, China
| | - Xiaoyi Wang
- First Affiliated Hospital, Huzhou University, Huzhou, China
| | - Jingwen Li
- School of Medicine & Nursing, Huzhou University, Huzhou, China
| | - Xiaoyu Li
- School of Medicine & Nursing, Huzhou University, Huzhou, China
| | - Jue Wang
- School of Medicine & Nursing, Huzhou University, Huzhou, China
| | - Yang Liu
- First Affiliated Hospital, Huzhou University, Huzhou, China
| | - Zhihong Wang
- Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, China
| | - Xiaobing Yang
- Third Affiliated Hospital, Huzhou University, Huzhou, China
| | - Jiapeng Gao
- Institute of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Juanjie Wu
- First Affiliated Hospital, Huzhou University, Huzhou, China
| | - Tao Sun
- Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, China
| | - Lixia Huo
- First Affiliated Hospital, Huzhou University, Huzhou, China
| | - Yanfeng Yi
- School of Life and Health Sciences, Huzhou College, Huzhou, China
| | - Jiantong Shen
- School of Medicine & Nursing, Huzhou University, Huzhou, China
| | - Jiexun Cai
- School of Medicine & Nursing, Huzhou University, Huzhou, China
| | - Yunliang Yao
- School of Medicine & Nursing, Huzhou University, Huzhou, China; First Affiliated Hospital, Huzhou University, Huzhou, China.
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192
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Chang Y, Liu J, Guo M, Ouyang W, Yan J, Xiong L, Li X. Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice. Genome Biol 2024; 25:262. [PMID: 39390531 PMCID: PMC11465533 DOI: 10.1186/s13059-024-03408-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 09/30/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND In response to drought stress (DS), plants undergo complex processes that entail significant transcriptome reprogramming. However, the intricate relationship between the dynamic alterations in the three-dimensional (3D) genome and the modulation of gene co-expression in drought responses remains a relatively unexplored area. RESULTS In this study, we reconstruct high-resolution 3D genome maps based on genomic regions marked by H3K9ac, an active histone modification that dynamically responds to soil water variations in rice. We discover a genome-wide disconnection of 3D genome contact upon DS with over 10,000 chromatin loops lost, which are partially recovered in the subsequent re-watering. Loops integrating promoter-promoter interactions (PPI) contribute to gene expression in addition to basal H3K9ac modifications. Moreover, H3K9ac-marked promoter regions with high affinities in mediating PPIs, termed as super-promoter regions (SPRs), integrate spatially clustered PPIs in a super-enhancer-like manner. Interestingly, the knockout mutation of OsbZIP23, a well-defined DS-responsive transcription factor, leads to the disassociation of over 80% DS-specific PPIs and decreased expression of the corresponding genes under DS. As a case study, we show how OsbZIP23 integrates the PPI cluster formation and the co-expression of four dehydrin genes, RAB16A-D, through targeting the RAB16C SPR in a stress signaling-dependent manner. CONCLUSIONS Our high-resolution 3D genome maps unveil the principles and details of dynamic genome folding in response to water supply variations and illustrate OsbZIP23 as an indispensable integrator of the yet unique 3D genome organization that is essential for gene co-expression under DS in rice.
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Affiliation(s)
- Yu Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiahan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minrong Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiapei Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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193
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Blanco P, Trigo da Roza F, Toribio-Celestino L, García-Pastor L, Caselli N, Morón Á, Ojeda F, Darracq B, Vergara E, Amaro F, San Millán Á, Skovgaard O, Mazel D, Loot C, Escudero JA. Chromosomal integrons are genetically and functionally isolated units of genomes. Nucleic Acids Res 2024:gkae866. [PMID: 39385642 DOI: 10.1093/nar/gkae866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 09/17/2024] [Accepted: 09/23/2024] [Indexed: 10/12/2024] Open
Abstract
Integrons are genetic elements that increase the evolvability of bacteria by capturing new genes and stockpiling them in arrays. Sedentary chromosomal integrons (SCIs) can be massive and highly stabilized structures encoding hundreds of genes, whose function remains generally unknown. SCIs have co-evolved with the host for aeons and are highly intertwined with their physiology from a mechanistic point of view. But, paradoxically, other aspects, like their variable content and location within the genome, suggest a high genetic and functional independence. In this work, we have explored the connection of SCIs to their host genome using as a model the Superintegron (SI), a 179-cassette long SCI in the genome of Vibrio cholerae N16961. We have relocated and deleted the SI using SeqDelTA, a novel method that allows to counteract the strong stabilization conferred by toxin-antitoxin systems within the array. We have characterized in depth the impact in V. cholerae's physiology, measuring fitness, chromosome replication dynamics, persistence, transcriptomics, phenomics, natural competence, virulence and resistance against protist grazing. The deletion of the SI did not produce detectable effects in any condition, proving that-despite millions of years of co-evolution-SCIs are genetically and functionally isolated units of genomes.
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Affiliation(s)
- Paula Blanco
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Filipa Trigo da Roza
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Laura Toribio-Celestino
- Departamento de Microbiología Microbiana, Centro Nacional de Biotecnología-CSIC, Madrid 28049, Spain
| | - Lucía García-Pastor
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Niccolò Caselli
- Departamento de Química Física, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro Morón
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Francisco Ojeda
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Ester Vergara
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Francisco Amaro
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro San Millán
- Departamento de Microbiología Microbiana, Centro Nacional de Biotecnología-CSIC, Madrid 28049, Spain
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - José Antonio Escudero
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
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194
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Hao D, Wang S, Feng L, Zhu S, Zhong Y, Zhang F, Chen Y, Fu Y, Shi Z, Tang F, Wu Y. Therapeutic effect of bloodletting on bone deterioration induced by hypobaric hypoxia in young rats. Bone 2024:117281. [PMID: 39395656 DOI: 10.1016/j.bone.2024.117281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 09/27/2024] [Accepted: 10/09/2024] [Indexed: 10/14/2024]
Abstract
OBJECTIVES High-altitude regions, comprising hypoxic conditions, are associated with different altitude-induced pathologies, including a reduction in bone density. Elucidating the mechanisms underlying bone degradation in such environments and developing targeted interventions and therapeutics is important. Bloodletting therapy has promising clinical applications, but its effects on the skeletal system and bone homeostasis are not well understood. The aim of this study was to investigate the effects of a hypobaric hypoxia environment on specific femoral morphological and structural properties, including bone volume, cortical thickness, and trabecular microarchitecture, in juvenile Sprague-Dawley (SD) rats, and to explore the potential modulating effects of a bloodletting intervention on these parameters. METHODS Male SD rats, 6 weeks of age, were subjected to a simulated hypobaric hypoxia environment, replicating a 5000-m altitude, for 12 weeks. For the bloodletting intervention group, rats were subjected to a weekly 500 μL tail vein blood withdrawal. Micro-CT technology, hematoxylin and eosin staining, and tartrate-resistant acid phosphatase staining were employed to comprehensively assess the femoral microstructure, tissue architecture, and cellular morphology. Additionally, immunofluorescence analysis was conducted to quantify the expression of key proteins, and transcriptome analysis was performed to identify differentially expressed genes. RESULTS Exposure of rats to hypobaric hypoxia led to a significant reduction in bone mineral content, trabecular bone number, and cortical bone thickness, suggesting a deterioration of bone microstructure. Additionally, the hypoxic environment upregulated the expression of RANKL and HIF-1α, while downregulating RUNX2. Notably, although bloodletting intervention did not significantly reverse these bone structural changes, transcriptome analysis revealed its regulatory influence on the expression of key genes, particularly Mmp2, Fosl2, and URS0000B2A65A, which are implicated in pathways governing the hypoxic response, osteoclast differentiation, and PI3K-Akt signaling. CONCLUSION This study highlights the detrimental effect of hypobaric hypoxia on the bone microstructure of juvenile rats and underscores the therapeutic potential of bloodletting to ameliorate this condition. Additionally, our study on the regulatory mechanisms mediating bloodletting's effects on gene expression offers fresh perspectives on bone alterations. It suggests promising avenues for the development of novel preventative measures and targeted therapies to address the challenges posed by related bone disorders.
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Affiliation(s)
- Doudou Hao
- Department of Biobank, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| | - Suyuan Wang
- Department of Biobank, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| | - Lin Feng
- Research Center for High Altitude Medicine, Qinghai University, Xining, China
| | - Suying Zhu
- Medical college, Tibet University, Lhasa, China
| | - Yang Zhong
- Department of Biobank, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| | - Fengying Zhang
- Department of Biobank, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| | - Yanli Chen
- Medical college, Xizang Minzu University, Xianyang, China
| | - Yongxing Fu
- Department of Cardiology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| | - Zhiyou Shi
- Medical college, Tibet University, Lhasa, China
| | - Feng Tang
- Research Center for High Altitude Medicine, Qinghai University, Xining, China; Qinghai-Utah Joint Research Key Lab for High Altitude Medicine, Qinghai University, Qinghai, Xining, China; Qinghai Provincial Key Laboratory of Plateau Medical Application, Key Laboratory of Ministry of Education, Qinghai University, Xining, China.
| | - Yunhong Wu
- Department of Endocrinology and Metabolism, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China.
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195
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Shipman GA, Padilla R, Horth C, Hu B, Bareke E, Vitorino FN, Gongora JM, Garcia BA, Lu C, Majewski J. Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation. Genome Biol 2024; 25:263. [PMID: 39390582 PMCID: PMC11465688 DOI: 10.1186/s13059-024-03415-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/01/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development and disease, how the molecular agents collectively shape the H3K36me landscape is unclear. RESULTS We use mouse mesenchymal stem cells to perturb the H3K36me methyltransferases (K36MTs) and infer the activities of the five most prominent enzymes: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it may also deposit H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other (K36MTs) prime gene bodies with lower methylation states ahead of transcription. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor. CONCLUSIONS Within genes, SETD2 primarily deposits H3K36me3, while the other K36MTs deposit H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1 > NSD2 > NSD3 > ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.
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Affiliation(s)
- Gerry A Shipman
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Reinnier Padilla
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Francisca N Vitorino
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joanna M Gongora
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Benjamin A Garcia
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada.
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196
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Pinkney HR, Ross CR, Hodgson TO, Pattison ST, Diermeier SD. Discovery of prognostic lncRNAs in colorectal cancer using spatial transcriptomics. NPJ Precis Oncol 2024; 8:230. [PMID: 39390212 PMCID: PMC11467462 DOI: 10.1038/s41698-024-00728-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 10/01/2024] [Indexed: 10/12/2024] Open
Abstract
Colorectal cancer (CRC) exhibits significant genetic and epigenetic diversity, evolving into sub-clonal populations with varied metastatic potentials and treatment responses. Predicting metastatic disease in CRC patients remains challenging, underscoring the need for reliable biomarkers. While most research on therapeutic targets and biomarkers has focused on proteins, non-coding RNAs such as long non-coding RNAs (lncRNAs) comprise most of the transcriptome and demonstrate superior tissue- and cancer-specific expression. We utilised spatial transcriptomics to investigate lncRNAs in CRC tumours, offering more precise cell-type-specific expression data compared to bulk RNA sequencing. Our analysis identified 301 lncRNAs linked to malignant CRC regions, which we validated with public data. Further validation using RNA-FISH revealed three lncRNAs (LINC01978, PLAC4, and LINC01303) that are detectable in stage II tumours but not in normal epithelium and are upregulated in metastatic tissues. These lncRNAs hold potential as biomarkers for early risk assessment of metastatic disease.
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Affiliation(s)
- Holly R Pinkney
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | | | | | - Sarah D Diermeier
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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197
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Fee BE, Fee LR, Menechella M, Affeldt B, Sprouse AR, Bounini A, Alwarawrah Y, Molloy CT, Ilkayeva OR, Prinz JA, Lenz DS, MacIver NJ, Rai P, Fessler MB, Coers J, Taylor GA. Type I interferon signaling and peroxisomal dysfunction contribute to enhanced inflammatory cytokine production in Irgm1-deficient macrophages. J Biol Chem 2024:107883. [PMID: 39395806 DOI: 10.1016/j.jbc.2024.107883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 09/30/2024] [Accepted: 10/05/2024] [Indexed: 10/14/2024] Open
Abstract
The human IRGM gene has been linked to inflammatory diseases including sepsis and Crohn's disease. Decreased expression of human IRGM, or of the mouse orthologues Irgm1 and Irgm2, leads to increased production of a number of inflammatory chemokines and cytokines in vivo and/or in cultured macrophages. Prior work has indicated that increased cytokine production is instigated by metabolic alterations and by changes in mitochondrial homeostasis; however, a comprehensive mechanism has not been elucidated. In the studies presented here, RNA deep sequencing and quantitative PCR were used to show that increases in cytokine production, as well as most changes in the transcriptional profile of Irgm1-/- bone marrow-derived macrophages (BMM), are dependent on increased type I IFN production seen in those cells. Metabolic alterations that drive increased cytokines in Irgm1-/- BMM - specifically increases in glycolysis and increased accumulation of acyl-carnitines - were unaffected by quenching type I IFN signaling. Dysregulation of peroxisomal homeostasis was identified as a novel upstream pathway that governs type I IFN production and inflammatory cytokine production. Collectively, these results enhance our understanding of the complex biochemical changes that are triggered by lack of Irgm1 and contribute to inflammatory disease seen with Irgm1-deficiency.
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Affiliation(s)
- Brian E Fee
- Department of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development; Duke University Medical Center, Durham, NC 27710
| | - Lanette R Fee
- Department of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development; Duke University Medical Center, Durham, NC 27710
| | - Mark Menechella
- Department of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development; Duke University Medical Center, Durham, NC 27710
| | - Bethann Affeldt
- Department of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development; Duke University Medical Center, Durham, NC 27710
| | - Aemilia R Sprouse
- Department of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development; Duke University Medical Center, Durham, NC 27710
| | - Amina Bounini
- Department of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development; Duke University Medical Center, Durham, NC 27710
| | - Yazan Alwarawrah
- Department of Pediatrics, Division of Pediatric Endocrinology and Diabetes, and Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599
| | - Caitlyn T Molloy
- Department of Pediatrics, Division of Pediatric Endocrinology and Diabetes, and Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599
| | - Olga R Ilkayeva
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701; Duke University School of Medicine, Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Durham, NC 27710
| | - Joseph A Prinz
- Duke University School of Medicine, Sequencing and Genomic Technologies, Durham, NC 27710
| | - Devi Swain Lenz
- Duke University School of Medicine, Sequencing and Genomic Technologies, Durham, NC 27710; Departments of Molecular Genetics and Microbiology; Duke University Medical Center, Durham, NC 27710
| | - Nancie J MacIver
- Department of Pediatrics, Division of Pediatric Endocrinology and Diabetes, and Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599
| | - Prashant Rai
- Immunity, Inflammation and Disease Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709
| | - Michael B Fessler
- Immunity, Inflammation and Disease Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709
| | - Jörn Coers
- Departments of Molecular Genetics and Microbiology; Duke University Medical Center, Durham, NC 27710; Department of Immunobiology; Duke University Medical Center, Durham, NC 27710
| | - Gregory A Taylor
- Department of Medicine, Division of Geriatrics, and Center for the Study of Aging and Human Development; Duke University Medical Center, Durham, NC 27710; Departments of Molecular Genetics and Microbiology; Duke University Medical Center, Durham, NC 27710; Department of Immunobiology; Duke University Medical Center, Durham, NC 27710; Geriatric Research, Education, and Clinical Center, Durham VA Health Care System, Durham, NC 27705.
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198
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Libert M, Quiquempoix S, Fain JS, Pyr Dit Ruys S, Haidar M, Wulleman M, Herinckx G, Vertommen D, Bouchart C, Arsenijevic T, Van Laethem JL, Jacquemin P. Stress granules are not present in Kras mutant cancers and do not control tumor growth. EMBO Rep 2024:10.1038/s44319-024-00284-6. [PMID: 39390257 DOI: 10.1038/s44319-024-00284-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 09/25/2024] [Accepted: 09/30/2024] [Indexed: 10/12/2024] Open
Abstract
Stress granules (SG) are membraneless ribonucleoprotein-based cytoplasmic organelles that assemble in response to stress. Their formation is often associated with an almost global suppression of translation, and the aberrant assembly or disassembly of these granules has pathological implications in neurodegeneration and cancer. In cancer, and particularly in the presence of oncogenic KRAS mutations, in vivo studies concluded that SG increase the resistance of cancer cells to stress. Hence, SG have recently been considered a promising target for therapy. Here, starting from our observations that genes coding for SG proteins are stimulated during development of pancreatic ductal adenocarcinoma, we analyze the formation of SG during tumorigenesis. We resort to in vitro, in vivo and in silico approaches, using mouse models, human samples and human data. Our analyses do not support that SG are formed during tumorigenesis of KRAS-driven cancers, at least that their presence is not universal, leading us to propose that caution is required before considering SG as therapeutic targets.
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Affiliation(s)
- Maxime Libert
- Université catholique de Louvain, de Duve Institute, 1200, Brussels, Belgium
| | - Sophie Quiquempoix
- Université catholique de Louvain, de Duve Institute, 1200, Brussels, Belgium
| | - Jean S Fain
- Université catholique de Louvain, de Duve Institute, 1200, Brussels, Belgium
| | | | - Malak Haidar
- Université catholique de Louvain, de Duve Institute, 1200, Brussels, Belgium
| | - Margaux Wulleman
- Université catholique de Louvain, de Duve Institute, 1200, Brussels, Belgium
| | - Gaëtan Herinckx
- Université catholique de Louvain, de Duve Institute, 1200, Brussels, Belgium
| | - Didier Vertommen
- Université catholique de Louvain, de Duve Institute, 1200, Brussels, Belgium
| | | | - Tatjana Arsenijevic
- Université libre de Bruxelles, Erasme University Hospital, Laboratory of Experimental Gastroenterology, Brussels, Belgium
| | - Jean-Luc Van Laethem
- Université libre de Bruxelles, Erasme University Hospital, Laboratory of Experimental Gastroenterology, Brussels, Belgium
| | - Patrick Jacquemin
- Université catholique de Louvain, de Duve Institute, 1200, Brussels, Belgium.
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199
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Zhou Z, Dong D, Yuan Y, Luo J, Liu XD, Chen LY, Wang G, Yin Y. Single cell atlas reveals multilayered metabolic heterogeneity across tumour types. EBioMedicine 2024; 109:105389. [PMID: 39393173 DOI: 10.1016/j.ebiom.2024.105389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/13/2024] Open
Abstract
BACKGROUND Metabolic reprogramming plays a pivotal role in cancer progression, contributing to substantial intratumour heterogeneity and influencing tumour behaviour. However, a systematic characterization of metabolic heterogeneity across multiple cancer types at the single-cell level remains limited. METHODS We integrated 296 tumour and normal samples spanning six common cancer types to construct a single-cell compendium of metabolic gene expression profiles and identify cell type-specific metabolic properties and reprogramming patterns. A computational approach based on non-negative matrix factorization (NMF) was utilised to identify metabolic meta-programs (MMPs) showing intratumour heterogeneity. In-vitro cell experiments were conducted to confirm the associations between MMPs and chemotherapy resistance, as well as the function of key metabolic regulators. Survival analyses were performed to assess clinical relevance of cellular metabolic properties. FINDINGS Our analysis revealed shared glycolysis upregulation and divergent regulation of citric acid cycle across different cell types. In malignant cells, we identified a colorectal cancer-specific MMP associated with resistance to the cuproptosis inducer elesclomol, validated through in-vitro cell experiments. Furthermore, our findings enabled the stratification of patients into distinct prognostic subtypes based on metabolic properties of specific cell types, such as myeloid cells. INTERPRETATION This study presents a nuanced understanding of multilayered metabolic heterogeneity, offering valuable insights into potential personalized therapies targeting tumour metabolism. FUNDING National Key Research and Development Program of China (2021YFA1300601). National Natural Science Foundation of China (key grants 82030081 and 81874235). The Shenzhen High-level Hospital Construction Fund and Shenzhen Basic Research Key Project (JCYJ20220818102811024). The Lam Chung Nin Foundation for Systems Biomedicine.
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Affiliation(s)
- Zhe Zhou
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Centre and School of Life Sciences, Peking University, Beijing 100191, China
| | - Di Dong
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Centre and School of Life Sciences, Peking University, Beijing 100191, China
| | - Yuyao Yuan
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Centre and School of Life Sciences, Peking University, Beijing 100191, China
| | - Juan Luo
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Xiao-Ding Liu
- Research Centre for Molecular Pathology, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100032, China
| | - Long-Yun Chen
- Research Centre for Molecular Pathology, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100032, China
| | - Guangxi Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Centre and School of Life Sciences, Peking University, Beijing 100191, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Centre and School of Life Sciences, Peking University, Beijing 100191, China.
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200
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Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq. Nat Protoc 2024:10.1038/s41596-024-01057-0. [PMID: 39390263 DOI: 10.1038/s41596-024-01057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/29/2024] [Indexed: 10/12/2024]
Abstract
The term 'RNA-seq' refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, single cells or single nuclei. The kallisto, bustools and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples or both. Additionally, these tools allow gene expression values to be classified as originating from nascent RNA species or mature RNA species, making this workflow amenable to both cell-based and nucleus-based assays. This protocol describes in detail how to use kallisto and bustools in conjunction with a wrapper, kb-python, to preprocess RNA-seq data. Execution of this protocol requires basic familiarity with a command line environment. With this protocol, quantification of a moderately sized RNA-seq dataset can be completed within minutes.
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Affiliation(s)
- Delaney K Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Laura Luebbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Lambda Moses
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Harold Pimentel
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A Sina Booeshaghi
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
| | - Páll Melsted
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland.
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland.
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
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